Galithil/gist:45b4fe6002d142243cc2103bfa9dffc8

## gistfile1.txt
Nov-14 16:09:25.687 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow -trace nextflow run ../NGI-RNAseq/main.nf -profile docker -c my_config --reads ./data/*R{1,2}.fastq.gz
Nov-14 16:09:25.763 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.22.3
Nov-14 16:09:25.781 [main] INFO  nextflow.cli.CmdRun - Launching `../NGI-RNAseq/main.nf` [stoic_booth] - revision: 1bc98d84bb
Nov-14 16:09:25.790 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/denismoreno/Documents/NGI-RNAseq/nextflow.config
Nov-14 16:09:25.792 [main] DEBUG nextflow.config.ConfigBuilder - User config file: my_config
Nov-14 16:09:25.793 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/denismoreno/Documents/NGI-RNAseq/nextflow.config
Nov-14 16:09:25.793 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/denismoreno/Documents/nextflow_test/my_config
Nov-14 16:09:26.078 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'docker'
Nov-14 16:09:26.109 [main] TRACE nextflow.config.ComposedConfigScript - Include config file: conf/docker.config [parent: /Users/denismoreno/Documents/NGI-RNAseq/nextflow.config]
Nov-14 16:09:26.216 [main] DEBUG nextflow.Session - Session uuid: 9328c5b5-b644-40a2-9ec8-4b04d87ccc75
Nov-14 16:09:26.216 [main] DEBUG nextflow.Session - Run name: stoic_booth
Nov-14 16:09:26.218 [main] DEBUG nextflow.Session - Executor pool size: 8
Nov-14 16:09:26.243 [main] DEBUG nextflow.cli.CmdRun -
  Version: 0.22.3 build 4095
  Modified: 12-10-2016 09:31 UTC (11:31 CEST)
  System: Mac OS X 10.11.6
  Runtime: Groovy 2.4.7 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14
  Encoding: UTF-8 (UTF-8)
  Process: 93771@130-229-6-39-dhcp.wlan.ki.se [130.229.6.39]
  CPUs: 8 - Mem: 16 GB (1.6 GB) - Swap: 12 GB (811.8 MB)  File systems: file, jar, s3
  JVM opts:
    -Xverify:none
    -Djava.library.path=
      /Users/denismoreno/Library/Java/Extensions
      /Library/Java/Extensions
      /Network/Library/Java/Extensions
      /System/Library/Java/Extensions
      /usr/lib/java
    -Dfile.encoding=UTF-8
    -Djava.awt.headless=true
  Capsule:
    capsule.app=nextflow_0.22.3
    capsule.jar=/Users/denismoreno/.nextflow/framework/0.22.3/nextflow-0.22.3-one.jar
  Environment:
    NXF_CLI=/usr/local/bin/nextflow -trace nextflow run ../NGI-RNAseq/main.nf -profile docker -c my_config --reads ./data/*R{1,2}.fastq.gz
    NXF_HOME=/Users/denismoreno/.nextflow
    NXF_ORG=nextflow-io
  Class-path:
    /Users/denismoreno/.nextflow/framework/0.22.3/nextflow-0.22.3-one.jar
    /Users/denismoreno/.nextflow/capsule/deps/io/nextflow/nextflow/0.22.3/nextflow-0.22.3.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/io/nextflow/nxf-commons/0.22.3/nxf-commons-0.22.3.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/groovy/groovy/2.4.7/groovy-2.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/groovy/groovy-nio/2.4.7/groovy-nio-2.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/groovy/groovy-json/2.4.7/groovy-json-2.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/groovy/groovy-templates/2.4.7/groovy-templates-2.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.21/jcl-over-slf4j-1.7.21.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/slf4j/jul-to-slf4j/1.7.21/jul-to-slf4j-1.7.21.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.21/log4j-over-slf4j-1.7.21.jar
    /Users/denismoreno/.nextflow/capsule/deps/ch/qos/logback/logback-classic/1.1.6/logback-classic-1.1.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/ch/qos/logback/logback-core/1.1.6/logback-core-1.1.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar
    /Users/denismoreno/.nextflow/capsule/deps/ch/grengine/grengine/1.0.3/grengine-1.0.3.jar
    /Users/denismoreno/.nextflow/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/iq80/leveldb/leveldb/0.7/leveldb-0.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.jar
    /Users/denismoreno/.nextflow/capsule/deps/io/nextflow/nxf-s3fs/1.0.0/nxf-s3fs-1.0.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk-s3/1.11.25/aws-java-sdk-s3-1.11.25.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk-ec2/1.11.25/aws-java-sdk-ec2-1.11.25.jar
    /Users/denismoreno/.nextflow/capsule/deps/javax/mail/mail/1.4.7/mail-1.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/google/guava/guava/16.0.1/guava-16.0.1.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/groovy/groovy-xml/2.4.7/groovy-xml-2.4.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/slf4j/slf4j-api/1.7.21/slf4j-api-1.7.21.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/codehaus/jsr166-mirror/jsr166y/1.7.0/jsr166y-1.7.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/iq80/leveldb/leveldb-api/0.7/leveldb-api-0.7.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/jcraft/jsch/0.1.53/jsch-0.1.53.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk-kms/1.11.25/aws-java-sdk-kms-1.11.25.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk-core/1.11.25/aws-java-sdk-core-1.11.25.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/amazonaws/jmespath-java/1.0/jmespath-java-1.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/javax/activation/activation/1.1/activation-1.1.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/fasterxml/jackson/core/jackson-databind/2.6.6/jackson-databind-2.6.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/fasterxml/jackson/dataformat/jackson-dataformat-cbor/2.6.6/jackson-dataformat-cbor-2.6.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/joda-time/joda-time/2.8.1/joda-time-2.8.1.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar
    /Users/denismoreno/.nextflow/capsule/deps/com/fasterxml/jackson/core/jackson-core/2.6.6/jackson-core-2.6.6.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/apache/httpcomponents/httpclient/4.5.2/httpclient-4.5.2.jar
    /Users/denismoreno/.nextflow/capsule/deps/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.jar
    /Users/denismoreno/.nextflow/capsule/deps/commons-codec/commons-codec/1.9/commons-codec-1.9.jar

Nov-14 16:09:26.254 [main] DEBUG nextflow.Session - Work-dir: /Users/denismoreno/Documents/nextflow_test/work [Mac OS X]
Nov-14 16:09:26.255 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/denismoreno/Documents/NGI-RNAseq/bin
Nov-14 16:09:26.328 [main] DEBUG nextflow.Session - Session start invoked
Nov-14 16:09:26.331 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Nov-14 16:09:26.331 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Nov-14 16:09:26.547 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@3381b4fc[org.codehaus.groovy.ast.expr.MethodCallExpression@6bea52d4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[downloadFASTA] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c42d2b7[org.codehaus.groovy.ast.expr.ClosureExpression@625abb97[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b1f29fa[org.codehaus.groovy.ast.stmt.ExpressionStatement@aeab9a1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40f70521[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@774698ab[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@55342f40[org.codehaus.groovy.ast.expr.MapEntryExpression@a4ca3f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72ea6193[]{ org.codehaus.groovy.ast.stmt.BlockStatement@31aa3ca5[org.codehaus.groovy.ast.stmt.ExpressionStatement@45905bff[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2a2c13a8[org.codehaus.groovy.ast.expr.BooleanExpression@b6b1987 ? org.codehaus.groovy.ast.expr.GStringExpression@6b44435b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2ccca26f[object: org.codehaus.groovy.ast.expr.VariableExpression@66b7550d[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@3543df7d(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7c541c15[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3542162a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@698122b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4212a0c8[org.codehaus.groovy.ast.expr.VariableExpression@1e7aa82b[variable: dl_url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b2c0e88[org.codehaus.groovy.ast.expr.PropertyExpression@5bd82fed[object: org.codehaus.groovy.ast.expr.VariableExpression@c1bd0be[variable: params] property: ConstantExpression[download_fasta]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@476b0ae6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c6804cd[object: org.codehaus.groovy.ast.expr.MethodCallExpression@655f7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@549949be[ConstantExpression[*.{fa,fasta}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3a45f1[org.codehaus.groovy.ast.expr.VariableExpression@17a87e37[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3eeb318f[expression:org.codehaus.groovy.ast.expr.GStringExpression@20a14b55[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@39ad977d[variable: dl_url]]]]] }]]]
Nov-14 16:09:26.551 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: downloadFASTA with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c42d2b7[org.codehaus.groovy.ast.expr.ClosureExpression@625abb97[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b1f29fa[org.codehaus.groovy.ast.stmt.ExpressionStatement@aeab9a1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40f70521[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@774698ab[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@55342f40[org.codehaus.groovy.ast.expr.MapEntryExpression@a4ca3f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72ea6193[]{ org.codehaus.groovy.ast.stmt.BlockStatement@31aa3ca5[org.codehaus.groovy.ast.stmt.ExpressionStatement@45905bff[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2a2c13a8[org.codehaus.groovy.ast.expr.BooleanExpression@b6b1987 ? org.codehaus.groovy.ast.expr.GStringExpression@6b44435b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2ccca26f[object: org.codehaus.groovy.ast.expr.VariableExpression@66b7550d[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@3543df7d(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7c541c15[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3542162a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@698122b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4212a0c8[org.codehaus.groovy.ast.expr.VariableExpression@1e7aa82b[variable: dl_url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b2c0e88[org.codehaus.groovy.ast.expr.PropertyExpression@5bd82fed[object: org.codehaus.groovy.ast.expr.VariableExpression@c1bd0be[variable: params] property: ConstantExpression[download_fasta]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@476b0ae6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c6804cd[object: org.codehaus.groovy.ast.expr.MethodCallExpression@655f7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@549949be[ConstantExpression[*.{fa,fasta}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3a45f1[org.codehaus.groovy.ast.expr.VariableExpression@17a87e37[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3eeb318f[expression:org.codehaus.groovy.ast.expr.GStringExpression@20a14b55[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@39ad977d[variable: dl_url]]]]] }]
Nov-14 16:09:26.551 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@77a98a6a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c42d2b7[ConstantExpression[downloadFASTA], org.codehaus.groovy.ast.expr.ClosureExpression@625abb97[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b1f29fa[org.codehaus.groovy.ast.stmt.ExpressionStatement@aeab9a1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40f70521[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@774698ab[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@55342f40[org.codehaus.groovy.ast.expr.MapEntryExpression@a4ca3f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72ea6193[]{ org.codehaus.groovy.ast.stmt.BlockStatement@31aa3ca5[org.codehaus.groovy.ast.stmt.ExpressionStatement@45905bff[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2a2c13a8[org.codehaus.groovy.ast.expr.BooleanExpression@b6b1987 ? org.codehaus.groovy.ast.expr.GStringExpression@6b44435b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2ccca26f[object: org.codehaus.groovy.ast.expr.VariableExpression@66b7550d[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@3543df7d(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7c541c15[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3542162a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@698122b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4212a0c8[org.codehaus.groovy.ast.expr.VariableExpression@1e7aa82b[variable: dl_url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b2c0e88[org.codehaus.groovy.ast.expr.PropertyExpression@5bd82fed[object: org.codehaus.groovy.ast.expr.VariableExpression@c1bd0be[variable: params] property: ConstantExpression[download_fasta]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@476b0ae6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c6804cd[object: org.codehaus.groovy.ast.expr.MethodCallExpression@655f7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@549949be[ConstantExpression[*.{fa,fasta}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3a45f1[org.codehaus.groovy.ast.expr.VariableExpression@17a87e37[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3eeb318f[expression:org.codehaus.groovy.ast.expr.GStringExpression@20a14b55[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@39ad977d[variable: dl_url]]]]] }]]
Nov-14 16:09:26.556 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3542162a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@698122b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4212a0c8[org.codehaus.groovy.ast.expr.VariableExpression@1e7aa82b[variable: dl_url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b2c0e88[org.codehaus.groovy.ast.expr.PropertyExpression@5bd82fed[object: org.codehaus.groovy.ast.expr.VariableExpression@c1bd0be[variable: params] property: ConstantExpression[download_fasta]]]]
Nov-14 16:09:26.556 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.556 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@698122b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4212a0c8[org.codehaus.groovy.ast.expr.VariableExpression@1e7aa82b[variable: dl_url]]]
Nov-14 16:09:26.556 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: val
Nov-14 16:09:26.557 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1c6804cd[object: org.codehaus.groovy.ast.expr.MethodCallExpression@655f7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@549949be[ConstantExpression[*.{fa,fasta}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3a45f1[org.codehaus.groovy.ast.expr.VariableExpression@17a87e37[variable: fasta]]]
Nov-14 16:09:26.557 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.557 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@655f7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@549949be[ConstantExpression[*.{fa,fasta}]]]
Nov-14 16:09:26.557 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.563 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@665df3c6[org.codehaus.groovy.ast.expr.MethodCallExpression@68b6f0d6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[downloadGTF] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4044fb95[org.codehaus.groovy.ast.expr.ClosureExpression@aa549e5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@36f48b4[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c00384f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b7ff809[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1bb564e2[org.codehaus.groovy.ast.expr.PropertyExpression@62e6b5c8[object: org.codehaus.groovy.ast.expr.VariableExpression@3f792b9b[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7b8233cd[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b20ca2b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@1cbf6e72[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@6aecbb8d[org.codehaus.groovy.ast.expr.MapEntryExpression@1af146(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@4da602fc[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2a8d39c4[org.codehaus.groovy.ast.stmt.ExpressionStatement@25b2cfcb[expression:org.codehaus.groovy.ast.expr.TernaryExpression@72758afa[org.codehaus.groovy.ast.expr.BooleanExpression@fb9c7aa ? org.codehaus.groovy.ast.expr.GStringExpression@4c398c80[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7fc6de5b[object: org.codehaus.groovy.ast.expr.VariableExpression@21baa903[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@607fbe09(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60a2630a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29df4d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5dd91bca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@40cb698e[org.codehaus.groovy.ast.expr.VariableExpression@3382f8ae[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60641ec8[org.codehaus.groovy.ast.expr.PropertyExpression@75f65e45[object: org.codehaus.groovy.ast.expr.VariableExpression@6eeade6c[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a891c97[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a5bd950[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4d18aa28[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75390459[ConstantExpression[*.gtf]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7756c3cd[org.codehaus.groovy.ast.expr.VariableExpression@2313052e[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2bd2b28e[expression:org.codehaus.groovy.ast.expr.GStringExpression@16746061[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@57fd91c9[variable: url]]]]] }]]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: downloadGTF with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@4044fb95[org.codehaus.groovy.ast.expr.ClosureExpression@aa549e5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@36f48b4[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c00384f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b7ff809[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1bb564e2[org.codehaus.groovy.ast.expr.PropertyExpression@62e6b5c8[object: org.codehaus.groovy.ast.expr.VariableExpression@3f792b9b[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7b8233cd[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b20ca2b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@1cbf6e72[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@6aecbb8d[org.codehaus.groovy.ast.expr.MapEntryExpression@1af146(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@4da602fc[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2a8d39c4[org.codehaus.groovy.ast.stmt.ExpressionStatement@25b2cfcb[expression:org.codehaus.groovy.ast.expr.TernaryExpression@72758afa[org.codehaus.groovy.ast.expr.BooleanExpression@fb9c7aa ? org.codehaus.groovy.ast.expr.GStringExpression@4c398c80[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7fc6de5b[object: org.codehaus.groovy.ast.expr.VariableExpression@21baa903[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@607fbe09(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60a2630a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29df4d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5dd91bca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@40cb698e[org.codehaus.groovy.ast.expr.VariableExpression@3382f8ae[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60641ec8[org.codehaus.groovy.ast.expr.PropertyExpression@75f65e45[object: org.codehaus.groovy.ast.expr.VariableExpression@6eeade6c[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a891c97[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a5bd950[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4d18aa28[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75390459[ConstantExpression[*.gtf]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7756c3cd[org.codehaus.groovy.ast.expr.VariableExpression@2313052e[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2bd2b28e[expression:org.codehaus.groovy.ast.expr.GStringExpression@16746061[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@57fd91c9[variable: url]]]]] }]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@6cfcd46d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4044fb95[ConstantExpression[downloadGTF], org.codehaus.groovy.ast.expr.ClosureExpression@aa549e5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@36f48b4[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c00384f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b7ff809[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1bb564e2[org.codehaus.groovy.ast.expr.PropertyExpression@62e6b5c8[object: org.codehaus.groovy.ast.expr.VariableExpression@3f792b9b[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7b8233cd[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b20ca2b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@1cbf6e72[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@6aecbb8d[org.codehaus.groovy.ast.expr.MapEntryExpression@1af146(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@4da602fc[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2a8d39c4[org.codehaus.groovy.ast.stmt.ExpressionStatement@25b2cfcb[expression:org.codehaus.groovy.ast.expr.TernaryExpression@72758afa[org.codehaus.groovy.ast.expr.BooleanExpression@fb9c7aa ? org.codehaus.groovy.ast.expr.GStringExpression@4c398c80[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7fc6de5b[object: org.codehaus.groovy.ast.expr.VariableExpression@21baa903[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@607fbe09(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60a2630a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29df4d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5dd91bca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@40cb698e[org.codehaus.groovy.ast.expr.VariableExpression@3382f8ae[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60641ec8[org.codehaus.groovy.ast.expr.PropertyExpression@75f65e45[object: org.codehaus.groovy.ast.expr.VariableExpression@6eeade6c[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a891c97[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a5bd950[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4d18aa28[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75390459[ConstantExpression[*.gtf]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7756c3cd[org.codehaus.groovy.ast.expr.VariableExpression@2313052e[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2bd2b28e[expression:org.codehaus.groovy.ast.expr.GStringExpression@16746061[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@57fd91c9[variable: url]]]]] }]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@29df4d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5dd91bca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@40cb698e[org.codehaus.groovy.ast.expr.VariableExpression@3382f8ae[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60641ec8[org.codehaus.groovy.ast.expr.PropertyExpression@75f65e45[object: org.codehaus.groovy.ast.expr.VariableExpression@6eeade6c[variable: params] property: ConstantExpression[downloadGTF]]]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5dd91bca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@40cb698e[org.codehaus.groovy.ast.expr.VariableExpression@3382f8ae[variable: url]]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: val
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@a5bd950[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4d18aa28[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75390459[ConstantExpression[*.gtf]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7756c3cd[org.codehaus.groovy.ast.expr.VariableExpression@2313052e[variable: gtf]]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4d18aa28[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75390459[ConstantExpression[*.gtf]]]
Nov-14 16:09:26.564 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.565 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@52045dbe[org.codehaus.groovy.ast.expr.MethodCallExpression@674658f7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[downloadGTF] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c8eee0f[org.codehaus.groovy.ast.expr.ClosureExpression@565b064f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@26425897[org.codehaus.groovy.ast.stmt.ExpressionStatement@73163d48[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@58c34bb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56a4479a[org.codehaus.groovy.ast.expr.PropertyExpression@62163b39[object: org.codehaus.groovy.ast.expr.VariableExpression@20a8a64e[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62f4ff3b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1698fc68[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@4504d271[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@207b8649[org.codehaus.groovy.ast.expr.MapEntryExpression@65b3a85a(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@34997338[]{ org.codehaus.groovy.ast.stmt.BlockStatement@57eda880[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b5825fa[expression:org.codehaus.groovy.ast.expr.TernaryExpression@53d1b9b3[org.codehaus.groovy.ast.expr.BooleanExpression@2cae1042 ? org.codehaus.groovy.ast.expr.GStringExpression@163d04ff[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7c209437[object: org.codehaus.groovy.ast.expr.VariableExpression@2262b621[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@7e928e2f(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f667fe[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@788fcafb[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4febb875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25e2a451[org.codehaus.groovy.ast.expr.VariableExpression@1698ee84[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c626be[org.codehaus.groovy.ast.expr.PropertyExpression@2fc0cc3[object: org.codehaus.groovy.ast.expr.VariableExpression@328cf0e1[variable: params] property: ConstantExpression[download_hisat2index]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63b1d4fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42e3ede4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@201b6b6f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75459c75[ConstantExpression[*/*.1.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@183e8023[org.codehaus.groovy.ast.expr.VariableExpression@45efc20d[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3e5499cc[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67ab1c47[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b78a709[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30bcf3c1[ConstantExpression[*/*.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3c96e3[org.codehaus.groovy.ast.expr.VariableExpression@15cafec7[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5b444398[expression:org.codehaus.groovy.ast.expr.GStringExpression@cb191ca[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        tar xzf *.tar.gz
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@42f48531[variable: url]]]]] }]]]
Nov-14 16:09:26.565 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: downloadGTF with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c8eee0f[org.codehaus.groovy.ast.expr.ClosureExpression@565b064f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@26425897[org.codehaus.groovy.ast.stmt.ExpressionStatement@73163d48[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@58c34bb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56a4479a[org.codehaus.groovy.ast.expr.PropertyExpression@62163b39[object: org.codehaus.groovy.ast.expr.VariableExpression@20a8a64e[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62f4ff3b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1698fc68[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@4504d271[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@207b8649[org.codehaus.groovy.ast.expr.MapEntryExpression@65b3a85a(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@34997338[]{ org.codehaus.groovy.ast.stmt.BlockStatement@57eda880[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b5825fa[expression:org.codehaus.groovy.ast.expr.TernaryExpression@53d1b9b3[org.codehaus.groovy.ast.expr.BooleanExpression@2cae1042 ? org.codehaus.groovy.ast.expr.GStringExpression@163d04ff[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7c209437[object: org.codehaus.groovy.ast.expr.VariableExpression@2262b621[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@7e928e2f(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f667fe[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@788fcafb[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4febb875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25e2a451[org.codehaus.groovy.ast.expr.VariableExpression@1698ee84[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c626be[org.codehaus.groovy.ast.expr.PropertyExpression@2fc0cc3[object: org.codehaus.groovy.ast.expr.VariableExpression@328cf0e1[variable: params] property: ConstantExpression[download_hisat2index]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63b1d4fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42e3ede4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@201b6b6f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75459c75[ConstantExpression[*/*.1.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@183e8023[org.codehaus.groovy.ast.expr.VariableExpression@45efc20d[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3e5499cc[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67ab1c47[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b78a709[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30bcf3c1[ConstantExpression[*/*.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3c96e3[org.codehaus.groovy.ast.expr.VariableExpression@15cafec7[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5b444398[expression:org.codehaus.groovy.ast.expr.GStringExpression@cb191ca[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        tar xzf *.tar.gz
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@42f48531[variable: url]]]]] }]
Nov-14 16:09:26.582 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@a776e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c8eee0f[ConstantExpression[downloadGTF], org.codehaus.groovy.ast.expr.ClosureExpression@565b064f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@26425897[org.codehaus.groovy.ast.stmt.ExpressionStatement@73163d48[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@58c34bb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56a4479a[org.codehaus.groovy.ast.expr.PropertyExpression@62163b39[object: org.codehaus.groovy.ast.expr.VariableExpression@20a8a64e[variable: params] property: ConstantExpression[downloadGTF]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62f4ff3b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1698fc68[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@4504d271[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@207b8649[org.codehaus.groovy.ast.expr.MapEntryExpression@65b3a85a(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@34997338[]{ org.codehaus.groovy.ast.stmt.BlockStatement@57eda880[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b5825fa[expression:org.codehaus.groovy.ast.expr.TernaryExpression@53d1b9b3[org.codehaus.groovy.ast.expr.BooleanExpression@2cae1042 ? org.codehaus.groovy.ast.expr.GStringExpression@163d04ff[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7c209437[object: org.codehaus.groovy.ast.expr.VariableExpression@2262b621[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@7e928e2f(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f667fe[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@788fcafb[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4febb875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25e2a451[org.codehaus.groovy.ast.expr.VariableExpression@1698ee84[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c626be[org.codehaus.groovy.ast.expr.PropertyExpression@2fc0cc3[object: org.codehaus.groovy.ast.expr.VariableExpression@328cf0e1[variable: params] property: ConstantExpression[download_hisat2index]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63b1d4fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42e3ede4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@201b6b6f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75459c75[ConstantExpression[*/*.1.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@183e8023[org.codehaus.groovy.ast.expr.VariableExpression@45efc20d[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3e5499cc[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67ab1c47[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b78a709[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30bcf3c1[ConstantExpression[*/*.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3c96e3[org.codehaus.groovy.ast.expr.VariableExpression@15cafec7[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5b444398[expression:org.codehaus.groovy.ast.expr.GStringExpression@cb191ca[strings: [ConstantExpression[
        curl -O -L ], ConstantExpression[
        tar xzf *.tar.gz
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@42f48531[variable: url]]]]] }]]
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@788fcafb[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4febb875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25e2a451[org.codehaus.groovy.ast.expr.VariableExpression@1698ee84[variable: url]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c626be[org.codehaus.groovy.ast.expr.PropertyExpression@2fc0cc3[object: org.codehaus.groovy.ast.expr.VariableExpression@328cf0e1[variable: params] property: ConstantExpression[download_hisat2index]]]]
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4febb875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25e2a451[org.codehaus.groovy.ast.expr.VariableExpression@1698ee84[variable: url]]]
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: val
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@42e3ede4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@201b6b6f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75459c75[ConstantExpression[*/*.1.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@183e8023[org.codehaus.groovy.ast.expr.VariableExpression@45efc20d[variable: hisat2_index]]]
Nov-14 16:09:26.583 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@201b6b6f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75459c75[ConstantExpression[*/*.1.ht2]]]
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@67ab1c47[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b78a709[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30bcf3c1[ConstantExpression[*/*.ht2]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3c96e3[org.codehaus.groovy.ast.expr.VariableExpression@15cafec7[variable: hs2_indices]]]
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@b78a709[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30bcf3c1[ConstantExpression[*/*.ht2]]]
Nov-14 16:09:26.584 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.586 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@792bbc74[org.codehaus.groovy.ast.expr.MethodCallExpression@79145d5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[makeSTARindex] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1f2f9244[org.codehaus.groovy.ast.expr.ClosureExpression@4c4d27c8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6821ea29[org.codehaus.groovy.ast.stmt.ExpressionStatement@338494fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@505a9d7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@758c83d8[org.codehaus.groovy.ast.expr.VariableExpression@129b4fe2[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5af3a0f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@19ae6bb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@10993713[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@58359ebd[org.codehaus.groovy.ast.expr.MapEntryExpression@24b6b8f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72cf2de5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2bb7bd00[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f031ebd[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4ee37ca3[org.codehaus.groovy.ast.expr.BooleanExpression@45c8d09f ? org.codehaus.groovy.ast.expr.GStringExpression@53812a9b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@14b030a0[object: org.codehaus.groovy.ast.expr.VariableExpression@41e350f1[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@422c3c7a(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@18230356[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@d8305c2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56bca85b[org.codehaus.groovy.ast.expr.ClosureExpression@75d0911a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@75e91545[org.codehaus.groovy.ast.stmt.ExpressionStatement@60d1a32f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@531c311e[org.codehaus.groovy.ast.expr.BooleanExpression@22b53226 ? org.codehaus.groovy.ast.expr.PropertyExpression@1fcb4808[object: org.codehaus.groovy.ast.expr.VariableExpression@726e5805[variable: params] property: ConstantExpression[makeSTARindex_cpus]] : ConstantExpression[12]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40c80397[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b672daa[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ea9b7c6[org.codehaus.groovy.ast.expr.ClosureExpression@e077866[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ed3068a[org.codehaus.groovy.ast.stmt.ExpressionStatement@7c2b6087[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fffff43[org.codehaus.groovy.ast.expr.BooleanExpression@a8e6492 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c7fd41f[object: org.codehaus.groovy.ast.expr.VariableExpression@3b77a04f[variable: params] property: ConstantExpression[makeSTARindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@7b324585[object: ConstantExpression[30] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e11485[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@60dce7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@662f5666[org.codehaus.groovy.ast.expr.ClosureExpression@fd8294b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5974109[org.codehaus.groovy.ast.stmt.ExpressionStatement@27305e6[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1ef3efa8[org.codehaus.groovy.ast.expr.BooleanExpression@502f1f4c ? org.codehaus.groovy.ast.expr.PropertyExpression@6f8f9349[object: org.codehaus.groovy.ast.expr.VariableExpression@75c9e76b[variable: params] property: ConstantExpression[makeSTARindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@7446d8d5[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5c3b6c6e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fbda97b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75f5fd58[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@37b70343[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@306851c7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@12bcd0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4879f0f2[org.codehaus.groovy.ast.expr.VariableExpression@47db5fa5[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@354fc8f0[org.codehaus.groovy.ast.expr.VariableExpression@41813449[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4678a2eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5b43fbf6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1080b026[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58ebfd03[org.codehaus.groovy.ast.expr.VariableExpression@5b07730f[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1fdfafd2[org.codehaus.groovy.ast.expr.VariableExpression@a4b2d8f[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@dcfda20[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6d304f9d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f73dcd6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c87bfe2[ConstantExpression[star]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fea7088[org.codehaus.groovy.ast.expr.VariableExpression@40499e4f[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@51cd7ffc[expression:org.codehaus.groovy.ast.expr.GStringExpression@30d4b288[strings: [ConstantExpression[
        mkdir star
        STAR \
            --runMode genomeGenerate \
            --runThreadN ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --sjdbOverhang 149 \
            --genomeDir star/ \
            --genomeFastaFiles ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@4cc6fa2a[object: org.codehaus.groovy.ast.expr.VariableExpression@40f1be1b[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@7a791b66[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@6f2cb653[variable: fasta]]]]] }]]]
Nov-14 16:09:26.588 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: makeSTARindex with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@1f2f9244[org.codehaus.groovy.ast.expr.ClosureExpression@4c4d27c8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6821ea29[org.codehaus.groovy.ast.stmt.ExpressionStatement@338494fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@505a9d7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@758c83d8[org.codehaus.groovy.ast.expr.VariableExpression@129b4fe2[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5af3a0f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@19ae6bb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@10993713[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@58359ebd[org.codehaus.groovy.ast.expr.MapEntryExpression@24b6b8f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72cf2de5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2bb7bd00[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f031ebd[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4ee37ca3[org.codehaus.groovy.ast.expr.BooleanExpression@45c8d09f ? org.codehaus.groovy.ast.expr.GStringExpression@53812a9b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@14b030a0[object: org.codehaus.groovy.ast.expr.VariableExpression@41e350f1[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@422c3c7a(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@18230356[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@d8305c2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56bca85b[org.codehaus.groovy.ast.expr.ClosureExpression@75d0911a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@75e91545[org.codehaus.groovy.ast.stmt.ExpressionStatement@60d1a32f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@531c311e[org.codehaus.groovy.ast.expr.BooleanExpression@22b53226 ? org.codehaus.groovy.ast.expr.PropertyExpression@1fcb4808[object: org.codehaus.groovy.ast.expr.VariableExpression@726e5805[variable: params] property: ConstantExpression[makeSTARindex_cpus]] : ConstantExpression[12]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40c80397[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b672daa[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ea9b7c6[org.codehaus.groovy.ast.expr.ClosureExpression@e077866[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ed3068a[org.codehaus.groovy.ast.stmt.ExpressionStatement@7c2b6087[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fffff43[org.codehaus.groovy.ast.expr.BooleanExpression@a8e6492 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c7fd41f[object: org.codehaus.groovy.ast.expr.VariableExpression@3b77a04f[variable: params] property: ConstantExpression[makeSTARindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@7b324585[object: ConstantExpression[30] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e11485[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@60dce7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@662f5666[org.codehaus.groovy.ast.expr.ClosureExpression@fd8294b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5974109[org.codehaus.groovy.ast.stmt.ExpressionStatement@27305e6[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1ef3efa8[org.codehaus.groovy.ast.expr.BooleanExpression@502f1f4c ? org.codehaus.groovy.ast.expr.PropertyExpression@6f8f9349[object: org.codehaus.groovy.ast.expr.VariableExpression@75c9e76b[variable: params] property: ConstantExpression[makeSTARindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@7446d8d5[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5c3b6c6e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fbda97b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75f5fd58[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@37b70343[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@306851c7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@12bcd0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4879f0f2[org.codehaus.groovy.ast.expr.VariableExpression@47db5fa5[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@354fc8f0[org.codehaus.groovy.ast.expr.VariableExpression@41813449[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4678a2eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5b43fbf6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1080b026[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58ebfd03[org.codehaus.groovy.ast.expr.VariableExpression@5b07730f[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1fdfafd2[org.codehaus.groovy.ast.expr.VariableExpression@a4b2d8f[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@dcfda20[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6d304f9d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f73dcd6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c87bfe2[ConstantExpression[star]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fea7088[org.codehaus.groovy.ast.expr.VariableExpression@40499e4f[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@51cd7ffc[expression:org.codehaus.groovy.ast.expr.GStringExpression@30d4b288[strings: [ConstantExpression[
        mkdir star
        STAR \
            --runMode genomeGenerate \
            --runThreadN ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --sjdbOverhang 149 \
            --genomeDir star/ \
            --genomeFastaFiles ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@4cc6fa2a[object: org.codehaus.groovy.ast.expr.VariableExpression@40f1be1b[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@7a791b66[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@6f2cb653[variable: fasta]]]]] }]
Nov-14 16:09:26.588 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@14c01636[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1f2f9244[ConstantExpression[makeSTARindex], org.codehaus.groovy.ast.expr.ClosureExpression@4c4d27c8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6821ea29[org.codehaus.groovy.ast.stmt.ExpressionStatement@338494fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@505a9d7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@758c83d8[org.codehaus.groovy.ast.expr.VariableExpression@129b4fe2[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5af3a0f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@19ae6bb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@10993713[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@58359ebd[org.codehaus.groovy.ast.expr.MapEntryExpression@24b6b8f6(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@72cf2de5[]{ org.codehaus.groovy.ast.stmt.BlockStatement@2bb7bd00[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f031ebd[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4ee37ca3[org.codehaus.groovy.ast.expr.BooleanExpression@45c8d09f ? org.codehaus.groovy.ast.expr.GStringExpression@53812a9b[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@14b030a0[object: org.codehaus.groovy.ast.expr.VariableExpression@41e350f1[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@422c3c7a(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@18230356[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@d8305c2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@56bca85b[org.codehaus.groovy.ast.expr.ClosureExpression@75d0911a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@75e91545[org.codehaus.groovy.ast.stmt.ExpressionStatement@60d1a32f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@531c311e[org.codehaus.groovy.ast.expr.BooleanExpression@22b53226 ? org.codehaus.groovy.ast.expr.PropertyExpression@1fcb4808[object: org.codehaus.groovy.ast.expr.VariableExpression@726e5805[variable: params] property: ConstantExpression[makeSTARindex_cpus]] : ConstantExpression[12]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40c80397[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4b672daa[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ea9b7c6[org.codehaus.groovy.ast.expr.ClosureExpression@e077866[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ed3068a[org.codehaus.groovy.ast.stmt.ExpressionStatement@7c2b6087[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fffff43[org.codehaus.groovy.ast.expr.BooleanExpression@a8e6492 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c7fd41f[object: org.codehaus.groovy.ast.expr.VariableExpression@3b77a04f[variable: params] property: ConstantExpression[makeSTARindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@7b324585[object: ConstantExpression[30] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e11485[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@60dce7ea[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@662f5666[org.codehaus.groovy.ast.expr.ClosureExpression@fd8294b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5974109[org.codehaus.groovy.ast.stmt.ExpressionStatement@27305e6[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1ef3efa8[org.codehaus.groovy.ast.expr.BooleanExpression@502f1f4c ? org.codehaus.groovy.ast.expr.PropertyExpression@6f8f9349[object: org.codehaus.groovy.ast.expr.VariableExpression@75c9e76b[variable: params] property: ConstantExpression[makeSTARindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@7446d8d5[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5c3b6c6e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fbda97b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75f5fd58[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@37b70343[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@306851c7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@12bcd0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4879f0f2[org.codehaus.groovy.ast.expr.VariableExpression@47db5fa5[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@354fc8f0[org.codehaus.groovy.ast.expr.VariableExpression@41813449[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4678a2eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5b43fbf6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1080b026[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58ebfd03[org.codehaus.groovy.ast.expr.VariableExpression@5b07730f[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1fdfafd2[org.codehaus.groovy.ast.expr.VariableExpression@a4b2d8f[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@dcfda20[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6d304f9d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f73dcd6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c87bfe2[ConstantExpression[star]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fea7088[org.codehaus.groovy.ast.expr.VariableExpression@40499e4f[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@51cd7ffc[expression:org.codehaus.groovy.ast.expr.GStringExpression@30d4b288[strings: [ConstantExpression[
        mkdir star
        STAR \
            --runMode genomeGenerate \
            --runThreadN ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --sjdbOverhang 149 \
            --genomeDir star/ \
            --genomeFastaFiles ], ConstantExpression[
        ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@4cc6fa2a[object: org.codehaus.groovy.ast.expr.VariableExpression@40f1be1b[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@7a791b66[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@6f2cb653[variable: fasta]]]]] }]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@306851c7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@12bcd0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4879f0f2[org.codehaus.groovy.ast.expr.VariableExpression@47db5fa5[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@354fc8f0[org.codehaus.groovy.ast.expr.VariableExpression@41813449[variable: fasta]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@12bcd0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4879f0f2[org.codehaus.groovy.ast.expr.VariableExpression@47db5fa5[variable: fasta]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5b43fbf6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1080b026[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58ebfd03[org.codehaus.groovy.ast.expr.VariableExpression@5b07730f[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1fdfafd2[org.codehaus.groovy.ast.expr.VariableExpression@a4b2d8f[variable: gtf]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1080b026[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58ebfd03[org.codehaus.groovy.ast.expr.VariableExpression@5b07730f[variable: gtf]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6d304f9d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f73dcd6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c87bfe2[ConstantExpression[star]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fea7088[org.codehaus.groovy.ast.expr.VariableExpression@40499e4f[variable: star_index]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@f73dcd6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c87bfe2[ConstantExpression[star]]]
Nov-14 16:09:26.589 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.592 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@6b9ce1bf[org.codehaus.groovy.ast.expr.MethodCallExpression@61884cb1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[makeHisatSplicesites] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75ed9710[org.codehaus.groovy.ast.expr.ClosureExpression@4fc5e095[]{ org.codehaus.groovy.ast.stmt.BlockStatement@435871cb[org.codehaus.groovy.ast.stmt.ExpressionStatement@609640d5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@79da1ec0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@19fb8826[org.codehaus.groovy.ast.expr.VariableExpression@192d74fb[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4bef0fe3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62ea3440[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@27953a83[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@556d0826[org.codehaus.groovy.ast.expr.MapEntryExpression@66ce957f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@55b5f5d2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5bfa8cc5[org.codehaus.groovy.ast.stmt.ExpressionStatement@666b83a4[expression:org.codehaus.groovy.ast.expr.TernaryExpression@749c877b[org.codehaus.groovy.ast.expr.BooleanExpression@efde75f ? org.codehaus.groovy.ast.expr.GStringExpression@16ecee1[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3b220bcb[object: org.codehaus.groovy.ast.expr.VariableExpression@2b95e48b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@4a3329b9(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddefd8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@160ac7fb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12bfd80d[org.codehaus.groovy.ast.expr.ClosureExpression@41925502[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13e3c1c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@5316e95f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3f053c80[org.codehaus.groovy.ast.expr.BooleanExpression@6c6c5427 ? org.codehaus.groovy.ast.expr.PropertyExpression@618c5d94[object: org.codehaus.groovy.ast.expr.VariableExpression@5b40ceb[variable: params] property: ConstantExpression[makeHisatSplicesites_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@13c3c1e1[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1d8062d2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e63ec0b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b956878[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@36546a22[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@285c08c8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@295eaa7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3918c187[org.codehaus.groovy.ast.expr.VariableExpression@2c88b9fc[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64dafeed[org.codehaus.groovy.ast.expr.VariableExpression@388ba540[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47605f2f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2ece4966[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1dd0e7c4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7894f09b[org.codehaus.groovy.ast.expr.GStringExpression@3d484181[strings: [ConstantExpression[], ConstantExpression[.hisat2_splice_sites.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6111ba37[object: org.codehaus.groovy.ast.expr.VariableExpression@7be58f16[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@242aa8d9[org.codehaus.groovy.ast.expr.VariableExpression@5b11a194[variable: indexing_splicesites], org.codehaus.groovy.ast.expr.VariableExpression@37bd68c3[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60f7cc1d[expression:org.codehaus.groovy.ast.expr.GStringExpression@11eadcba[strings: [ConstantExpression[
        hisat2_extract_splice_sites.py ], ConstantExpression[ > ], ConstantExpression[.hisat2_splice_sites.txt
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4721d212[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@1b065145[object: org.codehaus.groovy.ast.expr.VariableExpression@45cff11c[variable: gtf] property: ConstantExpression[baseName]]]]]] }]]]
Nov-14 16:09:26.592 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: makeHisatSplicesites with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@75ed9710[org.codehaus.groovy.ast.expr.ClosureExpression@4fc5e095[]{ org.codehaus.groovy.ast.stmt.BlockStatement@435871cb[org.codehaus.groovy.ast.stmt.ExpressionStatement@609640d5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@79da1ec0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@19fb8826[org.codehaus.groovy.ast.expr.VariableExpression@192d74fb[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4bef0fe3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62ea3440[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@27953a83[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@556d0826[org.codehaus.groovy.ast.expr.MapEntryExpression@66ce957f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@55b5f5d2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5bfa8cc5[org.codehaus.groovy.ast.stmt.ExpressionStatement@666b83a4[expression:org.codehaus.groovy.ast.expr.TernaryExpression@749c877b[org.codehaus.groovy.ast.expr.BooleanExpression@efde75f ? org.codehaus.groovy.ast.expr.GStringExpression@16ecee1[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3b220bcb[object: org.codehaus.groovy.ast.expr.VariableExpression@2b95e48b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@4a3329b9(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddefd8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@160ac7fb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12bfd80d[org.codehaus.groovy.ast.expr.ClosureExpression@41925502[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13e3c1c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@5316e95f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3f053c80[org.codehaus.groovy.ast.expr.BooleanExpression@6c6c5427 ? org.codehaus.groovy.ast.expr.PropertyExpression@618c5d94[object: org.codehaus.groovy.ast.expr.VariableExpression@5b40ceb[variable: params] property: ConstantExpression[makeHisatSplicesites_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@13c3c1e1[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1d8062d2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e63ec0b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b956878[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@36546a22[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@285c08c8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@295eaa7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3918c187[org.codehaus.groovy.ast.expr.VariableExpression@2c88b9fc[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64dafeed[org.codehaus.groovy.ast.expr.VariableExpression@388ba540[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47605f2f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2ece4966[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1dd0e7c4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7894f09b[org.codehaus.groovy.ast.expr.GStringExpression@3d484181[strings: [ConstantExpression[], ConstantExpression[.hisat2_splice_sites.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6111ba37[object: org.codehaus.groovy.ast.expr.VariableExpression@7be58f16[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@242aa8d9[org.codehaus.groovy.ast.expr.VariableExpression@5b11a194[variable: indexing_splicesites], org.codehaus.groovy.ast.expr.VariableExpression@37bd68c3[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60f7cc1d[expression:org.codehaus.groovy.ast.expr.GStringExpression@11eadcba[strings: [ConstantExpression[
        hisat2_extract_splice_sites.py ], ConstantExpression[ > ], ConstantExpression[.hisat2_splice_sites.txt
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4721d212[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@1b065145[object: org.codehaus.groovy.ast.expr.VariableExpression@45cff11c[variable: gtf] property: ConstantExpression[baseName]]]]]] }]
Nov-14 16:09:26.592 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@207ea13[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@75ed9710[ConstantExpression[makeHisatSplicesites], org.codehaus.groovy.ast.expr.ClosureExpression@4fc5e095[]{ org.codehaus.groovy.ast.stmt.BlockStatement@435871cb[org.codehaus.groovy.ast.stmt.ExpressionStatement@609640d5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@79da1ec0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@19fb8826[org.codehaus.groovy.ast.expr.VariableExpression@192d74fb[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4bef0fe3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62ea3440[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@27953a83[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@556d0826[org.codehaus.groovy.ast.expr.MapEntryExpression@66ce957f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@55b5f5d2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5bfa8cc5[org.codehaus.groovy.ast.stmt.ExpressionStatement@666b83a4[expression:org.codehaus.groovy.ast.expr.TernaryExpression@749c877b[org.codehaus.groovy.ast.expr.BooleanExpression@efde75f ? org.codehaus.groovy.ast.expr.GStringExpression@16ecee1[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3b220bcb[object: org.codehaus.groovy.ast.expr.VariableExpression@2b95e48b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@4a3329b9(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddefd8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@160ac7fb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12bfd80d[org.codehaus.groovy.ast.expr.ClosureExpression@41925502[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13e3c1c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@5316e95f[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3f053c80[org.codehaus.groovy.ast.expr.BooleanExpression@6c6c5427 ? org.codehaus.groovy.ast.expr.PropertyExpression@618c5d94[object: org.codehaus.groovy.ast.expr.VariableExpression@5b40ceb[variable: params] property: ConstantExpression[makeHisatSplicesites_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@13c3c1e1[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1d8062d2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e63ec0b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b956878[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@36546a22[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@285c08c8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@295eaa7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3918c187[org.codehaus.groovy.ast.expr.VariableExpression@2c88b9fc[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64dafeed[org.codehaus.groovy.ast.expr.VariableExpression@388ba540[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47605f2f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2ece4966[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1dd0e7c4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7894f09b[org.codehaus.groovy.ast.expr.GStringExpression@3d484181[strings: [ConstantExpression[], ConstantExpression[.hisat2_splice_sites.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6111ba37[object: org.codehaus.groovy.ast.expr.VariableExpression@7be58f16[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@242aa8d9[org.codehaus.groovy.ast.expr.VariableExpression@5b11a194[variable: indexing_splicesites], org.codehaus.groovy.ast.expr.VariableExpression@37bd68c3[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@60f7cc1d[expression:org.codehaus.groovy.ast.expr.GStringExpression@11eadcba[strings: [ConstantExpression[
        hisat2_extract_splice_sites.py ], ConstantExpression[ > ], ConstantExpression[.hisat2_splice_sites.txt
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4721d212[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@1b065145[object: org.codehaus.groovy.ast.expr.VariableExpression@45cff11c[variable: gtf] property: ConstantExpression[baseName]]]]]] }]]
Nov-14 16:09:26.592 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@285c08c8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@295eaa7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3918c187[org.codehaus.groovy.ast.expr.VariableExpression@2c88b9fc[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64dafeed[org.codehaus.groovy.ast.expr.VariableExpression@388ba540[variable: gtf]]]
Nov-14 16:09:26.592 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@295eaa7c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3918c187[org.codehaus.groovy.ast.expr.VariableExpression@2c88b9fc[variable: gtf]]]
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2ece4966[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1dd0e7c4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7894f09b[org.codehaus.groovy.ast.expr.GStringExpression@3d484181[strings: [ConstantExpression[], ConstantExpression[.hisat2_splice_sites.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@4bff1903null{ org.codehaus.groovy.ast.stmt.BlockStatement@62dae540[org.codehaus.groovy.ast.stmt.ExpressionStatement@5827af16[expression:org.codehaus.groovy.ast.expr.PropertyExpression@6111ba37[object: org.codehaus.groovy.ast.expr.VariableExpression@7be58f16[variable: gtf] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@242aa8d9[org.codehaus.groovy.ast.expr.VariableExpression@5b11a194[variable: indexing_splicesites], org.codehaus.groovy.ast.expr.VariableExpression@37bd68c3[variable: alignment_splicesites]]]
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1dd0e7c4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7894f09b[org.codehaus.groovy.ast.expr.GStringExpression@3d484181[strings: [ConstantExpression[], ConstantExpression[.hisat2_splice_sites.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@4bff1903null{ org.codehaus.groovy.ast.stmt.BlockStatement@62dae540[org.codehaus.groovy.ast.stmt.ExpressionStatement@5827af16[expression:org.codehaus.groovy.ast.expr.PropertyExpression@6111ba37[object: org.codehaus.groovy.ast.expr.VariableExpression@7be58f16[variable: gtf] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.593 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.595 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@56c9bbd8[org.codehaus.groovy.ast.expr.MethodCallExpression@630cb4a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[makeHISATindex] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@636e8cc[org.codehaus.groovy.ast.expr.ClosureExpression@f79a760[]{ org.codehaus.groovy.ast.stmt.BlockStatement@14f5da2c[org.codehaus.groovy.ast.stmt.ExpressionStatement@12dae582[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@239b0f9d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@619bfe29[org.codehaus.groovy.ast.expr.VariableExpression@5b057c8c[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1eb6749b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@652a7737[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b7ea70d[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@2bef51f2[org.codehaus.groovy.ast.expr.MapEntryExpression@650eab8(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@30f5a68a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1e1d3956[org.codehaus.groovy.ast.stmt.ExpressionStatement@4f2c9ba6[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4e28bdd1[org.codehaus.groovy.ast.expr.BooleanExpression@53f48368 ? org.codehaus.groovy.ast.expr.GStringExpression@24d4d7c9[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@f0e995e[object: org.codehaus.groovy.ast.expr.VariableExpression@4c37b5b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@73db4768(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@71b3bc45[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a8c1f44[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@150ab4ed[org.codehaus.groovy.ast.expr.ClosureExpression@3c435123[]{ org.codehaus.groovy.ast.stmt.BlockStatement@50fe837a[org.codehaus.groovy.ast.stmt.ExpressionStatement@3a62c01e[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7a8fa663[org.codehaus.groovy.ast.expr.BooleanExpression@5ce33a58 ? org.codehaus.groovy.ast.expr.PropertyExpression@78a287ed[object: org.codehaus.groovy.ast.expr.VariableExpression@546ccad7[variable: params] property: ConstantExpression[makeHISATindex_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5357c287[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1623134f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a527389[org.codehaus.groovy.ast.expr.ClosureExpression@485a3466[]{ org.codehaus.groovy.ast.stmt.BlockStatement@25748410[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b43529a[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4264b240[org.codehaus.groovy.ast.expr.BooleanExpression@5b04476e ? org.codehaus.groovy.ast.expr.PropertyExpression@5ad10c1a[object: org.codehaus.groovy.ast.expr.VariableExpression@6bb75258[variable: params] property: ConstantExpression[makeHISATindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@c260bdc[object: ConstantExpression[16] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@75e01201[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2783717b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76f7d241[org.codehaus.groovy.ast.expr.ClosureExpression@4a335fa8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f363cf5[org.codehaus.groovy.ast.stmt.ExpressionStatement@3829ac1[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4baf352a[org.codehaus.groovy.ast.expr.BooleanExpression@1bb1fde8 ? org.codehaus.groovy.ast.expr.PropertyExpression@15eebbff[object: org.codehaus.groovy.ast.expr.VariableExpression@22d6f11[variable: params] property: ConstantExpression[makeHISATindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@30990c1b[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2453f95d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@44828f6b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2dbe250d[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@553f1d75[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e1d8f9e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3e34ace1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62fe6067[org.codehaus.groovy.ast.expr.VariableExpression@4f071df8[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4de41af9[org.codehaus.groovy.ast.expr.VariableExpression@56ace400[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47404bea[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@305f7627[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5d018107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6cbcf243[org.codehaus.groovy.ast.expr.VariableExpression@29e6eb25[variable: indexing_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62435e70[org.codehaus.groovy.ast.expr.VariableExpression@339bf286[variable: indexing_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@38be305c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@269f4bad[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5ed731d0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3234f74e[org.codehaus.groovy.ast.expr.VariableExpression@7bc10d84[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@275fe372[org.codehaus.groovy.ast.expr.VariableExpression@40e10ff8[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@557a1e2d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@26a4842b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@7e38a7fe[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@366ef90e[org.codehaus.groovy.ast.expr.GStringExpression@33e01298[strings: [ConstantExpression[], ConstantExpression[.hisat2_index.1.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@31e75d13[object: org.codehaus.groovy.ast.expr.VariableExpression@a5b0b86[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3c354a[org.codehaus.groovy.ast.expr.VariableExpression@78fb9a67[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@73ff4fae[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@21aa6d6c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b968a76[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f9a01c1[org.codehaus.groovy.ast.expr.GStringExpression@2611b9a3[strings: [ConstantExpression[], ConstantExpression[.*.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@54227100[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5894c8[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1433046b[org.codehaus.groovy.ast.expr.VariableExpression@3f446bef[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7829b776[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5778826f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b64c4b7[variable: log] method: ConstantExpression[info] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4763c727[org.codehaus.groovy.ast.expr.GStringExpression@72445aba[strings: [ConstantExpression[[HISAT2 index build] Available memory: ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@61bcd567[object: org.codehaus.groovy.ast.expr.VariableExpression@1c80e49b[variable: task] property: ConstantExpression[memory]]]]]]], org.codehaus.groovy.ast.stmt.IfStatement@458342d3, org.codehaus.groovy.ast.stmt.ExpressionStatement@15c25153[expression:org.codehaus.groovy.ast.expr.GStringExpression@1252b961[strings: [ConstantExpression[
        ], ConstantExpression[
        hisat2-build -p ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[.hisat2_index
        touch ], ConstantExpression[.hisat2_index
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@9ed238c[variable: extract_exons], org.codehaus.groovy.ast.expr.PropertyExpression@56276db8[object: org.codehaus.groovy.ast.expr.VariableExpression@51e8e6e6[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@56f6d40b[variable: ss], org.codehaus.groovy.ast.expr.VariableExpression@36676c1a[variable: exon], org.codehaus.groovy.ast.expr.VariableExpression@5b408dc3[variable: fasta], org.codehaus.groovy.ast.expr.PropertyExpression@4d098f9b[object: org.codehaus.groovy.ast.expr.VariableExpression@2dbf4cbd[variable: fasta] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@20b5f2ac[object: org.codehaus.groovy.ast.expr.VariableExpression@7fc44dec[variable: fasta] property: ConstantExpression[baseName]]]]]] }]]]
Nov-14 16:09:26.595 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: makeHISATindex with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@636e8cc[org.codehaus.groovy.ast.expr.ClosureExpression@f79a760[]{ org.codehaus.groovy.ast.stmt.BlockStatement@14f5da2c[org.codehaus.groovy.ast.stmt.ExpressionStatement@12dae582[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@239b0f9d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@619bfe29[org.codehaus.groovy.ast.expr.VariableExpression@5b057c8c[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1eb6749b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@652a7737[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b7ea70d[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@2bef51f2[org.codehaus.groovy.ast.expr.MapEntryExpression@650eab8(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@30f5a68a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1e1d3956[org.codehaus.groovy.ast.stmt.ExpressionStatement@4f2c9ba6[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4e28bdd1[org.codehaus.groovy.ast.expr.BooleanExpression@53f48368 ? org.codehaus.groovy.ast.expr.GStringExpression@24d4d7c9[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@f0e995e[object: org.codehaus.groovy.ast.expr.VariableExpression@4c37b5b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@73db4768(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@71b3bc45[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a8c1f44[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@150ab4ed[org.codehaus.groovy.ast.expr.ClosureExpression@3c435123[]{ org.codehaus.groovy.ast.stmt.BlockStatement@50fe837a[org.codehaus.groovy.ast.stmt.ExpressionStatement@3a62c01e[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7a8fa663[org.codehaus.groovy.ast.expr.BooleanExpression@5ce33a58 ? org.codehaus.groovy.ast.expr.PropertyExpression@78a287ed[object: org.codehaus.groovy.ast.expr.VariableExpression@546ccad7[variable: params] property: ConstantExpression[makeHISATindex_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5357c287[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1623134f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a527389[org.codehaus.groovy.ast.expr.ClosureExpression@485a3466[]{ org.codehaus.groovy.ast.stmt.BlockStatement@25748410[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b43529a[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4264b240[org.codehaus.groovy.ast.expr.BooleanExpression@5b04476e ? org.codehaus.groovy.ast.expr.PropertyExpression@5ad10c1a[object: org.codehaus.groovy.ast.expr.VariableExpression@6bb75258[variable: params] property: ConstantExpression[makeHISATindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@c260bdc[object: ConstantExpression[16] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@75e01201[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2783717b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76f7d241[org.codehaus.groovy.ast.expr.ClosureExpression@4a335fa8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f363cf5[org.codehaus.groovy.ast.stmt.ExpressionStatement@3829ac1[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4baf352a[org.codehaus.groovy.ast.expr.BooleanExpression@1bb1fde8 ? org.codehaus.groovy.ast.expr.PropertyExpression@15eebbff[object: org.codehaus.groovy.ast.expr.VariableExpression@22d6f11[variable: params] property: ConstantExpression[makeHISATindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@30990c1b[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2453f95d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@44828f6b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2dbe250d[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@553f1d75[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e1d8f9e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3e34ace1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62fe6067[org.codehaus.groovy.ast.expr.VariableExpression@4f071df8[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4de41af9[org.codehaus.groovy.ast.expr.VariableExpression@56ace400[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47404bea[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@305f7627[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5d018107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6cbcf243[org.codehaus.groovy.ast.expr.VariableExpression@29e6eb25[variable: indexing_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62435e70[org.codehaus.groovy.ast.expr.VariableExpression@339bf286[variable: indexing_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@38be305c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@269f4bad[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5ed731d0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3234f74e[org.codehaus.groovy.ast.expr.VariableExpression@7bc10d84[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@275fe372[org.codehaus.groovy.ast.expr.VariableExpression@40e10ff8[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@557a1e2d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@26a4842b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@7e38a7fe[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@366ef90e[org.codehaus.groovy.ast.expr.GStringExpression@33e01298[strings: [ConstantExpression[], ConstantExpression[.hisat2_index.1.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@31e75d13[object: org.codehaus.groovy.ast.expr.VariableExpression@a5b0b86[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3c354a[org.codehaus.groovy.ast.expr.VariableExpression@78fb9a67[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@73ff4fae[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@21aa6d6c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b968a76[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f9a01c1[org.codehaus.groovy.ast.expr.GStringExpression@2611b9a3[strings: [ConstantExpression[], ConstantExpression[.*.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@54227100[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5894c8[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1433046b[org.codehaus.groovy.ast.expr.VariableExpression@3f446bef[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7829b776[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5778826f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b64c4b7[variable: log] method: ConstantExpression[info] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4763c727[org.codehaus.groovy.ast.expr.GStringExpression@72445aba[strings: [ConstantExpression[[HISAT2 index build] Available memory: ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@61bcd567[object: org.codehaus.groovy.ast.expr.VariableExpression@1c80e49b[variable: task] property: ConstantExpression[memory]]]]]]], org.codehaus.groovy.ast.stmt.IfStatement@458342d3, org.codehaus.groovy.ast.stmt.ExpressionStatement@15c25153[expression:org.codehaus.groovy.ast.expr.GStringExpression@1252b961[strings: [ConstantExpression[
        ], ConstantExpression[
        hisat2-build -p ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[.hisat2_index
        touch ], ConstantExpression[.hisat2_index
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@9ed238c[variable: extract_exons], org.codehaus.groovy.ast.expr.PropertyExpression@56276db8[object: org.codehaus.groovy.ast.expr.VariableExpression@51e8e6e6[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@56f6d40b[variable: ss], org.codehaus.groovy.ast.expr.VariableExpression@36676c1a[variable: exon], org.codehaus.groovy.ast.expr.VariableExpression@5b408dc3[variable: fasta], org.codehaus.groovy.ast.expr.PropertyExpression@4d098f9b[object: org.codehaus.groovy.ast.expr.VariableExpression@2dbf4cbd[variable: fasta] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@20b5f2ac[object: org.codehaus.groovy.ast.expr.VariableExpression@7fc44dec[variable: fasta] property: ConstantExpression[baseName]]]]]] }]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@7e3060d8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@636e8cc[ConstantExpression[makeHISATindex], org.codehaus.groovy.ast.expr.ClosureExpression@f79a760[]{ org.codehaus.groovy.ast.stmt.BlockStatement@14f5da2c[org.codehaus.groovy.ast.stmt.ExpressionStatement@12dae582[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@239b0f9d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@619bfe29[org.codehaus.groovy.ast.expr.VariableExpression@5b057c8c[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1eb6749b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@652a7737[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b7ea70d[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@2bef51f2[org.codehaus.groovy.ast.expr.MapEntryExpression@650eab8(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@30f5a68a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1e1d3956[org.codehaus.groovy.ast.stmt.ExpressionStatement@4f2c9ba6[expression:org.codehaus.groovy.ast.expr.TernaryExpression@4e28bdd1[org.codehaus.groovy.ast.expr.BooleanExpression@53f48368 ? org.codehaus.groovy.ast.expr.GStringExpression@24d4d7c9[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@f0e995e[object: org.codehaus.groovy.ast.expr.VariableExpression@4c37b5b[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@73db4768(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@71b3bc45[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@a8c1f44[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@150ab4ed[org.codehaus.groovy.ast.expr.ClosureExpression@3c435123[]{ org.codehaus.groovy.ast.stmt.BlockStatement@50fe837a[org.codehaus.groovy.ast.stmt.ExpressionStatement@3a62c01e[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7a8fa663[org.codehaus.groovy.ast.expr.BooleanExpression@5ce33a58 ? org.codehaus.groovy.ast.expr.PropertyExpression@78a287ed[object: org.codehaus.groovy.ast.expr.VariableExpression@546ccad7[variable: params] property: ConstantExpression[makeHISATindex_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5357c287[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1623134f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a527389[org.codehaus.groovy.ast.expr.ClosureExpression@485a3466[]{ org.codehaus.groovy.ast.stmt.BlockStatement@25748410[org.codehaus.groovy.ast.stmt.ExpressionStatement@2b43529a[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4264b240[org.codehaus.groovy.ast.expr.BooleanExpression@5b04476e ? org.codehaus.groovy.ast.expr.PropertyExpression@5ad10c1a[object: org.codehaus.groovy.ast.expr.VariableExpression@6bb75258[variable: params] property: ConstantExpression[makeHISATindex_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@c260bdc[object: ConstantExpression[16] property: ConstantExpression[GB]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@75e01201[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2783717b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76f7d241[org.codehaus.groovy.ast.expr.ClosureExpression@4a335fa8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f363cf5[org.codehaus.groovy.ast.stmt.ExpressionStatement@3829ac1[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4baf352a[org.codehaus.groovy.ast.expr.BooleanExpression@1bb1fde8 ? org.codehaus.groovy.ast.expr.PropertyExpression@15eebbff[object: org.codehaus.groovy.ast.expr.VariableExpression@22d6f11[variable: params] property: ConstantExpression[makeHISATindex_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@30990c1b[object: ConstantExpression[5] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2453f95d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@44828f6b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2dbe250d[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@553f1d75[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e1d8f9e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3e34ace1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62fe6067[org.codehaus.groovy.ast.expr.VariableExpression@4f071df8[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4de41af9[org.codehaus.groovy.ast.expr.VariableExpression@56ace400[variable: fasta]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47404bea[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@305f7627[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5d018107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6cbcf243[org.codehaus.groovy.ast.expr.VariableExpression@29e6eb25[variable: indexing_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62435e70[org.codehaus.groovy.ast.expr.VariableExpression@339bf286[variable: indexing_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@38be305c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@269f4bad[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5ed731d0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3234f74e[org.codehaus.groovy.ast.expr.VariableExpression@7bc10d84[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@275fe372[org.codehaus.groovy.ast.expr.VariableExpression@40e10ff8[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@557a1e2d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@26a4842b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@7e38a7fe[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@366ef90e[org.codehaus.groovy.ast.expr.GStringExpression@33e01298[strings: [ConstantExpression[], ConstantExpression[.hisat2_index.1.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@31e75d13[object: org.codehaus.groovy.ast.expr.VariableExpression@a5b0b86[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3c354a[org.codehaus.groovy.ast.expr.VariableExpression@78fb9a67[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@73ff4fae[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@21aa6d6c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b968a76[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f9a01c1[org.codehaus.groovy.ast.expr.GStringExpression@2611b9a3[strings: [ConstantExpression[], ConstantExpression[.*.ht2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@54227100[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5894c8[variable: fasta] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1433046b[org.codehaus.groovy.ast.expr.VariableExpression@3f446bef[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7829b776[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5778826f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b64c4b7[variable: log] method: ConstantExpression[info] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4763c727[org.codehaus.groovy.ast.expr.GStringExpression@72445aba[strings: [ConstantExpression[[HISAT2 index build] Available memory: ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@61bcd567[object: org.codehaus.groovy.ast.expr.VariableExpression@1c80e49b[variable: task] property: ConstantExpression[memory]]]]]]], org.codehaus.groovy.ast.stmt.IfStatement@458342d3, org.codehaus.groovy.ast.stmt.ExpressionStatement@15c25153[expression:org.codehaus.groovy.ast.expr.GStringExpression@1252b961[strings: [ConstantExpression[
        ], ConstantExpression[
        hisat2-build -p ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[ ], ConstantExpression[.hisat2_index
        touch ], ConstantExpression[.hisat2_index
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@9ed238c[variable: extract_exons], org.codehaus.groovy.ast.expr.PropertyExpression@56276db8[object: org.codehaus.groovy.ast.expr.VariableExpression@51e8e6e6[variable: task] property: ConstantExpression[cpus]], org.codehaus.groovy.ast.expr.VariableExpression@56f6d40b[variable: ss], org.codehaus.groovy.ast.expr.VariableExpression@36676c1a[variable: exon], org.codehaus.groovy.ast.expr.VariableExpression@5b408dc3[variable: fasta], org.codehaus.groovy.ast.expr.PropertyExpression@4d098f9b[object: org.codehaus.groovy.ast.expr.VariableExpression@2dbf4cbd[variable: fasta] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@20b5f2ac[object: org.codehaus.groovy.ast.expr.VariableExpression@7fc44dec[variable: fasta] property: ConstantExpression[baseName]]]]]] }]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6e1d8f9e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3e34ace1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62fe6067[org.codehaus.groovy.ast.expr.VariableExpression@4f071df8[variable: fasta]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4de41af9[org.codehaus.groovy.ast.expr.VariableExpression@56ace400[variable: fasta]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3e34ace1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62fe6067[org.codehaus.groovy.ast.expr.VariableExpression@4f071df8[variable: fasta]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@305f7627[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5d018107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6cbcf243[org.codehaus.groovy.ast.expr.VariableExpression@29e6eb25[variable: indexing_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@62435e70[org.codehaus.groovy.ast.expr.VariableExpression@339bf286[variable: indexing_splicesites]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5d018107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6cbcf243[org.codehaus.groovy.ast.expr.VariableExpression@29e6eb25[variable: indexing_splicesites]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@269f4bad[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5ed731d0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3234f74e[org.codehaus.groovy.ast.expr.VariableExpression@7bc10d84[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@275fe372[org.codehaus.groovy.ast.expr.VariableExpression@40e10ff8[variable: gtf]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5ed731d0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3234f74e[org.codehaus.groovy.ast.expr.VariableExpression@7bc10d84[variable: gtf]]]
Nov-14 16:09:26.596 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@26a4842b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@7e38a7fe[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@366ef90e[org.codehaus.groovy.ast.expr.GStringExpression@33e01298[strings: [ConstantExpression[], ConstantExpression[.hisat2_index.1.ht2]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@293d0107null{ org.codehaus.groovy.ast.stmt.BlockStatement@2692b61e[org.codehaus.groovy.ast.stmt.ExpressionStatement@7b64240d[expression:org.codehaus.groovy.ast.expr.PropertyExpression@31e75d13[object: org.codehaus.groovy.ast.expr.VariableExpression@a5b0b86[variable: fasta] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b3c354a[org.codehaus.groovy.ast.expr.VariableExpression@78fb9a67[variable: hisat2_index]]]
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@7e38a7fe[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@366ef90e[org.codehaus.groovy.ast.expr.GStringExpression@33e01298[strings: [ConstantExpression[], ConstantExpression[.hisat2_index.1.ht2]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@293d0107null{ org.codehaus.groovy.ast.stmt.BlockStatement@2692b61e[org.codehaus.groovy.ast.stmt.ExpressionStatement@7b64240d[expression:org.codehaus.groovy.ast.expr.PropertyExpression@31e75d13[object: org.codehaus.groovy.ast.expr.VariableExpression@a5b0b86[variable: fasta] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@21aa6d6c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@b968a76[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f9a01c1[org.codehaus.groovy.ast.expr.GStringExpression@2611b9a3[strings: [ConstantExpression[], ConstantExpression[.*.ht2]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@62fad19null{ org.codehaus.groovy.ast.stmt.BlockStatement@47dbb1e2[org.codehaus.groovy.ast.stmt.ExpressionStatement@74cadd41[expression:org.codehaus.groovy.ast.expr.PropertyExpression@54227100[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5894c8[variable: fasta] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1433046b[org.codehaus.groovy.ast.expr.VariableExpression@3f446bef[variable: hs2_indices]]]
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@b968a76[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f9a01c1[org.codehaus.groovy.ast.expr.GStringExpression@2611b9a3[strings: [ConstantExpression[], ConstantExpression[.*.ht2]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@62fad19null{ org.codehaus.groovy.ast.stmt.BlockStatement@47dbb1e2[org.codehaus.groovy.ast.stmt.ExpressionStatement@74cadd41[expression:org.codehaus.groovy.ast.expr.PropertyExpression@54227100[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5894c8[variable: fasta] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.597 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@2e54db99[org.codehaus.groovy.ast.expr.MethodCallExpression@55e8ec2f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[makeBED12] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4f2613d1[org.codehaus.groovy.ast.expr.ClosureExpression@6d24ffa1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@65a4798f[org.codehaus.groovy.ast.stmt.ExpressionStatement@773f7880[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@878452d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@426b6a74[org.codehaus.groovy.ast.expr.VariableExpression@4c51bb7[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@83298d7[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42a9e5d1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b080f3a[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@773cbf4f[org.codehaus.groovy.ast.expr.MapEntryExpression@6b54655f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@665e9289[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7d3430a7[org.codehaus.groovy.ast.stmt.ExpressionStatement@6f603e89[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2756c0a7[org.codehaus.groovy.ast.expr.BooleanExpression@350ec41e ? org.codehaus.groovy.ast.expr.GStringExpression@69637b10[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71984c3[object: org.codehaus.groovy.ast.expr.VariableExpression@165b2f7f[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@5536379e(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@277f7dd3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c8bca63[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2364305a[org.codehaus.groovy.ast.expr.ClosureExpression@470a696f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bc715b8[org.codehaus.groovy.ast.stmt.ExpressionStatement@292d1c71[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2b491fee[org.codehaus.groovy.ast.expr.BooleanExpression@3f1c5af9 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c55f277[object: org.codehaus.groovy.ast.expr.VariableExpression@5ddabb18[variable: params] property: ConstantExpression[makeBED12_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@3e8f7922[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63192798[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50eca7c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58e6d4b8[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1de5f0ef[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@376a312c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28d6290[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ca0256d[org.codehaus.groovy.ast.expr.VariableExpression@5ef0d29e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@38f57b3d[org.codehaus.groovy.ast.expr.VariableExpression@51850751[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3ce3db41[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@64df9a61[object: org.codehaus.groovy.ast.expr.MethodCallExpression@77602954[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@e260766[org.codehaus.groovy.ast.expr.GStringExpression@2c3dec30[strings: [ConstantExpression[], ConstantExpression[.bed]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@34a97744[object: org.codehaus.groovy.ast.expr.VariableExpression@4275c20c[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c56e013[org.codehaus.groovy.ast.expr.VariableExpression@3fc9dfc5[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40258c2f[expression:org.codehaus.groovy.ast.expr.GStringExpression@2cac4385[strings: [ConstantExpression[
        convert2bed \
            --input=gtf \
            --output=bed \
            --max-mem=], ConstantExpression[G \
            < ], ConstantExpression[ > ], ConstantExpression[.bed
        ]] values: [org.codehaus.groovy.ast.expr.MethodCallExpression@6731787b[object: org.codehaus.groovy.ast.expr.PropertyExpression@16f7b4af[object: org.codehaus.groovy.ast.expr.VariableExpression@7adf16aa[variable: task] property: ConstantExpression[memory]] method: ConstantExpression[toGiga] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@34a1d21f[]], org.codehaus.groovy.ast.expr.VariableExpression@58bf8650[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@73c60324[object: org.codehaus.groovy.ast.expr.VariableExpression@71ae31b0[variable: gtf] property: ConstantExpression[baseName]]]]]] }]]]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: makeBED12 with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@4f2613d1[org.codehaus.groovy.ast.expr.ClosureExpression@6d24ffa1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@65a4798f[org.codehaus.groovy.ast.stmt.ExpressionStatement@773f7880[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@878452d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@426b6a74[org.codehaus.groovy.ast.expr.VariableExpression@4c51bb7[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@83298d7[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42a9e5d1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b080f3a[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@773cbf4f[org.codehaus.groovy.ast.expr.MapEntryExpression@6b54655f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@665e9289[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7d3430a7[org.codehaus.groovy.ast.stmt.ExpressionStatement@6f603e89[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2756c0a7[org.codehaus.groovy.ast.expr.BooleanExpression@350ec41e ? org.codehaus.groovy.ast.expr.GStringExpression@69637b10[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71984c3[object: org.codehaus.groovy.ast.expr.VariableExpression@165b2f7f[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@5536379e(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@277f7dd3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c8bca63[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2364305a[org.codehaus.groovy.ast.expr.ClosureExpression@470a696f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bc715b8[org.codehaus.groovy.ast.stmt.ExpressionStatement@292d1c71[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2b491fee[org.codehaus.groovy.ast.expr.BooleanExpression@3f1c5af9 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c55f277[object: org.codehaus.groovy.ast.expr.VariableExpression@5ddabb18[variable: params] property: ConstantExpression[makeBED12_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@3e8f7922[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63192798[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50eca7c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58e6d4b8[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1de5f0ef[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@376a312c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28d6290[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ca0256d[org.codehaus.groovy.ast.expr.VariableExpression@5ef0d29e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@38f57b3d[org.codehaus.groovy.ast.expr.VariableExpression@51850751[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3ce3db41[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@64df9a61[object: org.codehaus.groovy.ast.expr.MethodCallExpression@77602954[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@e260766[org.codehaus.groovy.ast.expr.GStringExpression@2c3dec30[strings: [ConstantExpression[], ConstantExpression[.bed]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@34a97744[object: org.codehaus.groovy.ast.expr.VariableExpression@4275c20c[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c56e013[org.codehaus.groovy.ast.expr.VariableExpression@3fc9dfc5[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40258c2f[expression:org.codehaus.groovy.ast.expr.GStringExpression@2cac4385[strings: [ConstantExpression[
        convert2bed \
            --input=gtf \
            --output=bed \
            --max-mem=], ConstantExpression[G \
            < ], ConstantExpression[ > ], ConstantExpression[.bed
        ]] values: [org.codehaus.groovy.ast.expr.MethodCallExpression@6731787b[object: org.codehaus.groovy.ast.expr.PropertyExpression@16f7b4af[object: org.codehaus.groovy.ast.expr.VariableExpression@7adf16aa[variable: task] property: ConstantExpression[memory]] method: ConstantExpression[toGiga] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@34a1d21f[]], org.codehaus.groovy.ast.expr.VariableExpression@58bf8650[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@73c60324[object: org.codehaus.groovy.ast.expr.VariableExpression@71ae31b0[variable: gtf] property: ConstantExpression[baseName]]]]]] }]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@4ba534b0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4f2613d1[ConstantExpression[makeBED12], org.codehaus.groovy.ast.expr.ClosureExpression@6d24ffa1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@65a4798f[org.codehaus.groovy.ast.stmt.ExpressionStatement@773f7880[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@878452d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@426b6a74[org.codehaus.groovy.ast.expr.VariableExpression@4c51bb7[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@83298d7[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@42a9e5d1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.TupleExpression@5b080f3a[org.codehaus.groovy.ast.expr.NamedArgumentListExpression@773cbf4f[org.codehaus.groovy.ast.expr.MapEntryExpression@6b54655f(key: ConstantExpression[path], value: org.codehaus.groovy.ast.expr.ClosureExpression@665e9289[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7d3430a7[org.codehaus.groovy.ast.stmt.ExpressionStatement@6f603e89[expression:org.codehaus.groovy.ast.expr.TernaryExpression@2756c0a7[org.codehaus.groovy.ast.expr.BooleanExpression@350ec41e ? org.codehaus.groovy.ast.expr.GStringExpression@69637b10[strings: [ConstantExpression[], ConstantExpression[/reference_genome]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71984c3[object: org.codehaus.groovy.ast.expr.VariableExpression@165b2f7f[variable: params] property: ConstantExpression[outdir]]]] : ConstantExpression[null]]]] }), org.codehaus.groovy.ast.expr.MapEntryExpression@5536379e(key: ConstantExpression[mode], value: ConstantExpression[copy])]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@277f7dd3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c8bca63[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2364305a[org.codehaus.groovy.ast.expr.ClosureExpression@470a696f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bc715b8[org.codehaus.groovy.ast.stmt.ExpressionStatement@292d1c71[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2b491fee[org.codehaus.groovy.ast.expr.BooleanExpression@3f1c5af9 ? org.codehaus.groovy.ast.expr.PropertyExpression@1c55f277[object: org.codehaus.groovy.ast.expr.VariableExpression@5ddabb18[variable: params] property: ConstantExpression[makeBED12_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@3e8f7922[object: ConstantExpression[2] property: ConstantExpression[h]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63192798[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50eca7c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58e6d4b8[ConstantExpression[terminate]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1de5f0ef[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@376a312c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28d6290[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ca0256d[org.codehaus.groovy.ast.expr.VariableExpression@5ef0d29e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@38f57b3d[org.codehaus.groovy.ast.expr.VariableExpression@51850751[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3ce3db41[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@64df9a61[object: org.codehaus.groovy.ast.expr.MethodCallExpression@77602954[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@e260766[org.codehaus.groovy.ast.expr.GStringExpression@2c3dec30[strings: [ConstantExpression[], ConstantExpression[.bed]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@34a97744[object: org.codehaus.groovy.ast.expr.VariableExpression@4275c20c[variable: gtf] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c56e013[org.codehaus.groovy.ast.expr.VariableExpression@3fc9dfc5[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@40258c2f[expression:org.codehaus.groovy.ast.expr.GStringExpression@2cac4385[strings: [ConstantExpression[
        convert2bed \
            --input=gtf \
            --output=bed \
            --max-mem=], ConstantExpression[G \
            < ], ConstantExpression[ > ], ConstantExpression[.bed
        ]] values: [org.codehaus.groovy.ast.expr.MethodCallExpression@6731787b[object: org.codehaus.groovy.ast.expr.PropertyExpression@16f7b4af[object: org.codehaus.groovy.ast.expr.VariableExpression@7adf16aa[variable: task] property: ConstantExpression[memory]] method: ConstantExpression[toGiga] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@34a1d21f[]], org.codehaus.groovy.ast.expr.VariableExpression@58bf8650[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@73c60324[object: org.codehaus.groovy.ast.expr.VariableExpression@71ae31b0[variable: gtf] property: ConstantExpression[baseName]]]]]] }]]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@376a312c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28d6290[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ca0256d[org.codehaus.groovy.ast.expr.VariableExpression@5ef0d29e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@38f57b3d[org.codehaus.groovy.ast.expr.VariableExpression@51850751[variable: gtf]]]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@28d6290[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ca0256d[org.codehaus.groovy.ast.expr.VariableExpression@5ef0d29e[variable: gtf]]]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@64df9a61[object: org.codehaus.groovy.ast.expr.MethodCallExpression@77602954[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@e260766[org.codehaus.groovy.ast.expr.GStringExpression@2c3dec30[strings: [ConstantExpression[], ConstantExpression[.bed]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@6f0ca692null{ org.codehaus.groovy.ast.stmt.BlockStatement@2c104774[org.codehaus.groovy.ast.stmt.ExpressionStatement@2cb3d0f7[expression:org.codehaus.groovy.ast.expr.PropertyExpression@34a97744[object: org.codehaus.groovy.ast.expr.VariableExpression@4275c20c[variable: gtf] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c56e013[org.codehaus.groovy.ast.expr.VariableExpression@3fc9dfc5[variable: bed12]]]
Nov-14 16:09:26.600 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.601 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@77602954[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@e260766[org.codehaus.groovy.ast.expr.GStringExpression@2c3dec30[strings: [ConstantExpression[], ConstantExpression[.bed]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@6f0ca692null{ org.codehaus.groovy.ast.stmt.BlockStatement@2c104774[org.codehaus.groovy.ast.stmt.ExpressionStatement@2cb3d0f7[expression:org.codehaus.groovy.ast.expr.PropertyExpression@34a97744[object: org.codehaus.groovy.ast.expr.VariableExpression@4275c20c[variable: gtf] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.601 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.602 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@4e517165[org.codehaus.groovy.ast.expr.MethodCallExpression@44e3760b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[fastqc] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6a66a204[org.codehaus.groovy.ast.expr.ClosureExpression@5860f3d7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1d7f7be7[org.codehaus.groovy.ast.stmt.ExpressionStatement@42f3156d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ddae9b5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@427b5f92[org.codehaus.groovy.ast.expr.MapExpression@24bdb479[org.codehaus.groovy.ast.expr.MapEntryExpression@7e3f95fe(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@34625ccd[strings: [ConstantExpression[], ConstantExpression[/fastqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2c7d121c[object: org.codehaus.groovy.ast.expr.VariableExpression@65aa6596[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67389cb8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@419a20a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@533377b[org.codehaus.groovy.ast.expr.ClosureExpression@3383649e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@10fde30a[org.codehaus.groovy.ast.stmt.ExpressionStatement@f27ea3[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1ce61929[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@346939bf[org.codehaus.groovy.ast.expr.BooleanExpression@4bf3798b ? org.codehaus.groovy.ast.expr.PropertyExpression@58670130[object: org.codehaus.groovy.ast.expr.VariableExpression@74e47444[variable: params] property: ConstantExpression[fastqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@9bd0fa6[object: ConstantExpression[2] property: ConstantExpression[GB]]]("*" at 331:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@59d2103b[object: org.codehaus.groovy.ast.expr.VariableExpression@39dcf4b0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6e4de19b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f6c03cb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@46f699d5[org.codehaus.groovy.ast.expr.ClosureExpression@18518ccf[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1991f767[org.codehaus.groovy.ast.stmt.ExpressionStatement@768ccdc5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4c6daf0[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@10650953[org.codehaus.groovy.ast.expr.BooleanExpression@659eef7 ? org.codehaus.groovy.ast.expr.PropertyExpression@162be91c[object: org.codehaus.groovy.ast.expr.VariableExpression@2488b073[variable: params] property: ConstantExpression[fastqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c9f0a20[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 332:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@55787112[object: org.codehaus.groovy.ast.expr.VariableExpression@1cd201a8[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7db82169[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1992eaf4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f74e835[org.codehaus.groovy.ast.expr.ClosureExpression@3276732[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f28bd56[org.codehaus.groovy.ast.stmt.ExpressionStatement@31e3250d[expression:org.codehaus.groovy.ast.expr.TernaryExpression@19fe4644[org.codehaus.groovy.ast.expr.BooleanExpression@21d8bcbe ? ConstantExpression[retry] : ConstantExpression[ignore]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5be067de[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7383eae2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@18245eb0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c7d3c46[org.codehaus.groovy.ast.expr.MethodCallExpression@24fb6a80[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@48c35007[org.codehaus.groovy.ast.expr.VariableExpression@72a85671[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@6722db6e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18f20260[org.codehaus.groovy.ast.expr.VariableExpression@4ae33a11[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a48e6e2[org.codehaus.groovy.ast.expr.VariableExpression@b40bb6e[variable: read_files_fastqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a94964[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5049d8b2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6d0b5baf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@631e06ab[ConstantExpression[*_fastqc.{zip,html}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3591c5[org.codehaus.groovy.ast.expr.VariableExpression@34a75079[variable: fastqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@346a361[expression:org.codehaus.groovy.ast.expr.GStringExpression@107ed6fc[strings: [ConstantExpression[
    fastqc -q ], ConstantExpression[
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1643d68f[variable: reads]]]]] }]]]
Nov-14 16:09:26.602 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: fastqc with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@6a66a204[org.codehaus.groovy.ast.expr.ClosureExpression@5860f3d7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1d7f7be7[org.codehaus.groovy.ast.stmt.ExpressionStatement@42f3156d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ddae9b5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@427b5f92[org.codehaus.groovy.ast.expr.MapExpression@24bdb479[org.codehaus.groovy.ast.expr.MapEntryExpression@7e3f95fe(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@34625ccd[strings: [ConstantExpression[], ConstantExpression[/fastqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2c7d121c[object: org.codehaus.groovy.ast.expr.VariableExpression@65aa6596[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67389cb8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@419a20a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@533377b[org.codehaus.groovy.ast.expr.ClosureExpression@3383649e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@10fde30a[org.codehaus.groovy.ast.stmt.ExpressionStatement@f27ea3[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1ce61929[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@346939bf[org.codehaus.groovy.ast.expr.BooleanExpression@4bf3798b ? org.codehaus.groovy.ast.expr.PropertyExpression@58670130[object: org.codehaus.groovy.ast.expr.VariableExpression@74e47444[variable: params] property: ConstantExpression[fastqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@9bd0fa6[object: ConstantExpression[2] property: ConstantExpression[GB]]]("*" at 331:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@59d2103b[object: org.codehaus.groovy.ast.expr.VariableExpression@39dcf4b0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6e4de19b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f6c03cb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@46f699d5[org.codehaus.groovy.ast.expr.ClosureExpression@18518ccf[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1991f767[org.codehaus.groovy.ast.stmt.ExpressionStatement@768ccdc5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4c6daf0[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@10650953[org.codehaus.groovy.ast.expr.BooleanExpression@659eef7 ? org.codehaus.groovy.ast.expr.PropertyExpression@162be91c[object: org.codehaus.groovy.ast.expr.VariableExpression@2488b073[variable: params] property: ConstantExpression[fastqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c9f0a20[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 332:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@55787112[object: org.codehaus.groovy.ast.expr.VariableExpression@1cd201a8[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7db82169[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1992eaf4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f74e835[org.codehaus.groovy.ast.expr.ClosureExpression@3276732[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f28bd56[org.codehaus.groovy.ast.stmt.ExpressionStatement@31e3250d[expression:org.codehaus.groovy.ast.expr.TernaryExpression@19fe4644[org.codehaus.groovy.ast.expr.BooleanExpression@21d8bcbe ? ConstantExpression[retry] : ConstantExpression[ignore]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5be067de[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7383eae2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@18245eb0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c7d3c46[org.codehaus.groovy.ast.expr.MethodCallExpression@24fb6a80[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@48c35007[org.codehaus.groovy.ast.expr.VariableExpression@72a85671[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@6722db6e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18f20260[org.codehaus.groovy.ast.expr.VariableExpression@4ae33a11[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a48e6e2[org.codehaus.groovy.ast.expr.VariableExpression@b40bb6e[variable: read_files_fastqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a94964[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5049d8b2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6d0b5baf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@631e06ab[ConstantExpression[*_fastqc.{zip,html}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3591c5[org.codehaus.groovy.ast.expr.VariableExpression@34a75079[variable: fastqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@346a361[expression:org.codehaus.groovy.ast.expr.GStringExpression@107ed6fc[strings: [ConstantExpression[
    fastqc -q ], ConstantExpression[
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1643d68f[variable: reads]]]]] }]
Nov-14 16:09:26.603 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@186978a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6a66a204[ConstantExpression[fastqc], org.codehaus.groovy.ast.expr.ClosureExpression@5860f3d7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1d7f7be7[org.codehaus.groovy.ast.stmt.ExpressionStatement@42f3156d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ddae9b5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@427b5f92[org.codehaus.groovy.ast.expr.MapExpression@24bdb479[org.codehaus.groovy.ast.expr.MapEntryExpression@7e3f95fe(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@34625ccd[strings: [ConstantExpression[], ConstantExpression[/fastqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2c7d121c[object: org.codehaus.groovy.ast.expr.VariableExpression@65aa6596[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67389cb8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@419a20a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@533377b[org.codehaus.groovy.ast.expr.ClosureExpression@3383649e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@10fde30a[org.codehaus.groovy.ast.stmt.ExpressionStatement@f27ea3[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1ce61929[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@346939bf[org.codehaus.groovy.ast.expr.BooleanExpression@4bf3798b ? org.codehaus.groovy.ast.expr.PropertyExpression@58670130[object: org.codehaus.groovy.ast.expr.VariableExpression@74e47444[variable: params] property: ConstantExpression[fastqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@9bd0fa6[object: ConstantExpression[2] property: ConstantExpression[GB]]]("*" at 331:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@59d2103b[object: org.codehaus.groovy.ast.expr.VariableExpression@39dcf4b0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6e4de19b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f6c03cb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@46f699d5[org.codehaus.groovy.ast.expr.ClosureExpression@18518ccf[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1991f767[org.codehaus.groovy.ast.stmt.ExpressionStatement@768ccdc5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4c6daf0[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@10650953[org.codehaus.groovy.ast.expr.BooleanExpression@659eef7 ? org.codehaus.groovy.ast.expr.PropertyExpression@162be91c[object: org.codehaus.groovy.ast.expr.VariableExpression@2488b073[variable: params] property: ConstantExpression[fastqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c9f0a20[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 332:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@55787112[object: org.codehaus.groovy.ast.expr.VariableExpression@1cd201a8[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7db82169[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1992eaf4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f74e835[org.codehaus.groovy.ast.expr.ClosureExpression@3276732[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3f28bd56[org.codehaus.groovy.ast.stmt.ExpressionStatement@31e3250d[expression:org.codehaus.groovy.ast.expr.TernaryExpression@19fe4644[org.codehaus.groovy.ast.expr.BooleanExpression@21d8bcbe ? ConstantExpression[retry] : ConstantExpression[ignore]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5be067de[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7383eae2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@18245eb0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c7d3c46[org.codehaus.groovy.ast.expr.MethodCallExpression@24fb6a80[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@48c35007[org.codehaus.groovy.ast.expr.VariableExpression@72a85671[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@6722db6e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18f20260[org.codehaus.groovy.ast.expr.VariableExpression@4ae33a11[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a48e6e2[org.codehaus.groovy.ast.expr.VariableExpression@b40bb6e[variable: read_files_fastqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a94964[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5049d8b2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6d0b5baf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@631e06ab[ConstantExpression[*_fastqc.{zip,html}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3591c5[org.codehaus.groovy.ast.expr.VariableExpression@34a75079[variable: fastqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@346a361[expression:org.codehaus.groovy.ast.expr.GStringExpression@107ed6fc[strings: [ConstantExpression[
    fastqc -q ], ConstantExpression[
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1643d68f[variable: reads]]]]] }]]
Nov-14 16:09:26.603 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@7383eae2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@18245eb0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c7d3c46[org.codehaus.groovy.ast.expr.MethodCallExpression@24fb6a80[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@48c35007[org.codehaus.groovy.ast.expr.VariableExpression@72a85671[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@6722db6e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18f20260[org.codehaus.groovy.ast.expr.VariableExpression@4ae33a11[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a48e6e2[org.codehaus.groovy.ast.expr.VariableExpression@b40bb6e[variable: read_files_fastqc]]]
Nov-14 16:09:26.603 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.603 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@18245eb0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c7d3c46[org.codehaus.groovy.ast.expr.MethodCallExpression@24fb6a80[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@48c35007[org.codehaus.groovy.ast.expr.VariableExpression@72a85671[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@6722db6e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18f20260[org.codehaus.groovy.ast.expr.VariableExpression@4ae33a11[variable: reads]]]]]
Nov-14 16:09:26.603 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: set
Nov-14 16:09:26.604 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5049d8b2[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6d0b5baf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@631e06ab[ConstantExpression[*_fastqc.{zip,html}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a3591c5[org.codehaus.groovy.ast.expr.VariableExpression@34a75079[variable: fastqc_results]]]
Nov-14 16:09:26.604 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.604 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6d0b5baf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@631e06ab[ConstantExpression[*_fastqc.{zip,html}]]]
Nov-14 16:09:26.604 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.606 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@297ea53a[org.codehaus.groovy.ast.expr.MethodCallExpression@acb0951[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[trim_galore] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bf22f18[org.codehaus.groovy.ast.expr.ClosureExpression@267f474e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a7471ce[org.codehaus.groovy.ast.stmt.ExpressionStatement@28276e50[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62e70ea3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3efe7086[org.codehaus.groovy.ast.expr.MapExpression@675d8c96[org.codehaus.groovy.ast.expr.MapEntryExpression@741b3bc3(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2ed3b1f5[strings: [ConstantExpression[], ConstantExpression[/trim_galore]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@63648ee9[object: org.codehaus.groovy.ast.expr.VariableExpression@68d6972f[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@45be7cd5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7651218e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3185fa6b[org.codehaus.groovy.ast.expr.ClosureExpression@6d366c9b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b58ed3c[org.codehaus.groovy.ast.stmt.ExpressionStatement@24faea88[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3a320ade[org.codehaus.groovy.ast.expr.BooleanExpression@64beebb7 ? org.codehaus.groovy.ast.expr.PropertyExpression@7813cb11[object: org.codehaus.groovy.ast.expr.VariableExpression@bcec031[variable: params] property: ConstantExpression[trim_galore_cpus]] : ConstantExpression[2]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21005f6c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@32f0fba8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@545de5a4[org.codehaus.groovy.ast.expr.ClosureExpression@29ef6856[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ab7a938[org.codehaus.groovy.ast.stmt.ExpressionStatement@3faf2e7d[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4648ce9[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@569bf9eb[org.codehaus.groovy.ast.expr.BooleanExpression@61526469 ? org.codehaus.groovy.ast.expr.PropertyExpression@274872f8[object: org.codehaus.groovy.ast.expr.VariableExpression@76ba13c[variable: params] property: ConstantExpression[trim_galore_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@eb6449b[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 355:50:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7c351808[object: org.codehaus.groovy.ast.expr.VariableExpression@180e6ac4[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42b64ab8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7e985ce9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a39fe6a[org.codehaus.groovy.ast.expr.ClosureExpression@410ae9a3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@319988b0[org.codehaus.groovy.ast.stmt.ExpressionStatement@d5ae57e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@68759011[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7e242b4d[org.codehaus.groovy.ast.expr.BooleanExpression@305f031 ? org.codehaus.groovy.ast.expr.PropertyExpression@592e843a[object: org.codehaus.groovy.ast.expr.VariableExpression@1d1f7216[variable: params] property: ConstantExpression[trim_galore_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@423e4cbb[object: ConstantExpression[8] property: ConstantExpression[h]]]("*" at 356:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6e16b8b5[object: org.codehaus.groovy.ast.expr.VariableExpression@43b4fe19[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25ddbbbb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1536602f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4ebea12c[org.codehaus.groovy.ast.expr.ClosureExpression@2a1edad4[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6256ac4f[org.codehaus.groovy.ast.stmt.ExpressionStatement@44c79f32[expression:org.codehaus.groovy.ast.expr.TernaryExpression@7fcbe147[org.codehaus.groovy.ast.expr.BooleanExpression@235f4c10 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@743cb8e0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c7a975a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2c1b9e4b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@757d6814[org.codehaus.groovy.ast.expr.MethodCallExpression@649725e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3c0fae6c[org.codehaus.groovy.ast.expr.VariableExpression@4c168660[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@52b56a3e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@fd0e5b6[org.codehaus.groovy.ast.expr.VariableExpression@4eed46ee[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b0fcd5[org.codehaus.groovy.ast.expr.VariableExpression@4fad94a7[variable: read_files_trimming]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@475835b1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6326d182[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5241cf67[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@716a7124[ConstantExpression[*fq.gz]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@77192705[org.codehaus.groovy.ast.expr.VariableExpression@226642a5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7e809b79[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5cc126dc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@625e134e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72bd06ca[ConstantExpression[*trimming_report.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@89c10b7[org.codehaus.groovy.ast.expr.VariableExpression@5dbe30be[variable: trimgalore_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4fe89c24[expression:org.codehaus.groovy.ast.expr.BinaryExpression@55795845[org.codehaus.groovy.ast.expr.VariableExpression@3d08f3f5[variable: single]("=" at 367:12:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@119f1f2a[org.codehaus.groovy.ast.expr.VariableExpression@1a1da881[variable: reads]("instanceof" at 367:20:  "instanceof" )org.codehaus.groovy.ast.expr.ClassExpression@5b970f7[type: Path]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7fd4acee[expression:org.codehaus.groovy.ast.expr.BinaryExpression@165b8a71[org.codehaus.groovy.ast.expr.VariableExpression@6175619b[variable: c_r1]("=" at 368:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@2f058b8a[org.codehaus.groovy.ast.expr.BooleanExpression@756cf158 ? org.codehaus.groovy.ast.expr.GStringExpression@3f2ef586[strings: [ConstantExpression[--clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@751d3241[object: org.codehaus.groovy.ast.expr.VariableExpression@76c7beb3[variable: params] property: ConstantExpression[clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@64337702[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2cf92cc7[org.codehaus.groovy.ast.expr.VariableExpression@30ea8c23[variable: c_r2]("=" at 369:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@7b139eab[org.codehaus.groovy.ast.expr.BooleanExpression@4e76dac ? org.codehaus.groovy.ast.expr.GStringExpression@611df6e3[strings: [ConstantExpression[--clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5f2f577[object: org.codehaus.groovy.ast.expr.VariableExpression@6273c5a4[variable: params] property: ConstantExpression[clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5d465e4b[expression:org.codehaus.groovy.ast.expr.BinaryExpression@53e211ee[org.codehaus.groovy.ast.expr.VariableExpression@41a90fa8[variable: tpc_r1]("=" at 370:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@3d8bbcdc[org.codehaus.groovy.ast.expr.BooleanExpression@52500920 ? org.codehaus.groovy.ast.expr.GStringExpression@117e0fe5[strings: [ConstantExpression[--three_prime_clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@18a3962d[object: org.codehaus.groovy.ast.expr.VariableExpression@78aea4b9[variable: params] property: ConstantExpression[three_prime_clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a65bb85[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4b85880b[org.codehaus.groovy.ast.expr.VariableExpression@4f936da8[variable: tpc_r2]("=" at 371:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@4215838f[org.codehaus.groovy.ast.expr.BooleanExpression@452ba1db ? org.codehaus.groovy.ast.expr.GStringExpression@2289aca5[strings: [ConstantExpression[--three_prime_clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76a36b71[object: org.codehaus.groovy.ast.expr.VariableExpression@184497d1[variable: params] property: ConstantExpression[three_prime_clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.IfStatement@f9d87b] }]]]
Nov-14 16:09:26.606 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: trim_galore with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bf22f18[org.codehaus.groovy.ast.expr.ClosureExpression@267f474e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a7471ce[org.codehaus.groovy.ast.stmt.ExpressionStatement@28276e50[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62e70ea3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3efe7086[org.codehaus.groovy.ast.expr.MapExpression@675d8c96[org.codehaus.groovy.ast.expr.MapEntryExpression@741b3bc3(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2ed3b1f5[strings: [ConstantExpression[], ConstantExpression[/trim_galore]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@63648ee9[object: org.codehaus.groovy.ast.expr.VariableExpression@68d6972f[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@45be7cd5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7651218e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3185fa6b[org.codehaus.groovy.ast.expr.ClosureExpression@6d366c9b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b58ed3c[org.codehaus.groovy.ast.stmt.ExpressionStatement@24faea88[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3a320ade[org.codehaus.groovy.ast.expr.BooleanExpression@64beebb7 ? org.codehaus.groovy.ast.expr.PropertyExpression@7813cb11[object: org.codehaus.groovy.ast.expr.VariableExpression@bcec031[variable: params] property: ConstantExpression[trim_galore_cpus]] : ConstantExpression[2]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21005f6c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@32f0fba8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@545de5a4[org.codehaus.groovy.ast.expr.ClosureExpression@29ef6856[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ab7a938[org.codehaus.groovy.ast.stmt.ExpressionStatement@3faf2e7d[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4648ce9[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@569bf9eb[org.codehaus.groovy.ast.expr.BooleanExpression@61526469 ? org.codehaus.groovy.ast.expr.PropertyExpression@274872f8[object: org.codehaus.groovy.ast.expr.VariableExpression@76ba13c[variable: params] property: ConstantExpression[trim_galore_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@eb6449b[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 355:50:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7c351808[object: org.codehaus.groovy.ast.expr.VariableExpression@180e6ac4[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42b64ab8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7e985ce9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a39fe6a[org.codehaus.groovy.ast.expr.ClosureExpression@410ae9a3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@319988b0[org.codehaus.groovy.ast.stmt.ExpressionStatement@d5ae57e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@68759011[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7e242b4d[org.codehaus.groovy.ast.expr.BooleanExpression@305f031 ? org.codehaus.groovy.ast.expr.PropertyExpression@592e843a[object: org.codehaus.groovy.ast.expr.VariableExpression@1d1f7216[variable: params] property: ConstantExpression[trim_galore_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@423e4cbb[object: ConstantExpression[8] property: ConstantExpression[h]]]("*" at 356:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6e16b8b5[object: org.codehaus.groovy.ast.expr.VariableExpression@43b4fe19[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25ddbbbb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1536602f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4ebea12c[org.codehaus.groovy.ast.expr.ClosureExpression@2a1edad4[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6256ac4f[org.codehaus.groovy.ast.stmt.ExpressionStatement@44c79f32[expression:org.codehaus.groovy.ast.expr.TernaryExpression@7fcbe147[org.codehaus.groovy.ast.expr.BooleanExpression@235f4c10 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@743cb8e0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c7a975a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2c1b9e4b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@757d6814[org.codehaus.groovy.ast.expr.MethodCallExpression@649725e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3c0fae6c[org.codehaus.groovy.ast.expr.VariableExpression@4c168660[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@52b56a3e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@fd0e5b6[org.codehaus.groovy.ast.expr.VariableExpression@4eed46ee[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b0fcd5[org.codehaus.groovy.ast.expr.VariableExpression@4fad94a7[variable: read_files_trimming]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@475835b1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6326d182[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5241cf67[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@716a7124[ConstantExpression[*fq.gz]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@77192705[org.codehaus.groovy.ast.expr.VariableExpression@226642a5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7e809b79[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5cc126dc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@625e134e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72bd06ca[ConstantExpression[*trimming_report.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@89c10b7[org.codehaus.groovy.ast.expr.VariableExpression@5dbe30be[variable: trimgalore_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4fe89c24[expression:org.codehaus.groovy.ast.expr.BinaryExpression@55795845[org.codehaus.groovy.ast.expr.VariableExpression@3d08f3f5[variable: single]("=" at 367:12:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@119f1f2a[org.codehaus.groovy.ast.expr.VariableExpression@1a1da881[variable: reads]("instanceof" at 367:20:  "instanceof" )org.codehaus.groovy.ast.expr.ClassExpression@5b970f7[type: Path]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7fd4acee[expression:org.codehaus.groovy.ast.expr.BinaryExpression@165b8a71[org.codehaus.groovy.ast.expr.VariableExpression@6175619b[variable: c_r1]("=" at 368:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@2f058b8a[org.codehaus.groovy.ast.expr.BooleanExpression@756cf158 ? org.codehaus.groovy.ast.expr.GStringExpression@3f2ef586[strings: [ConstantExpression[--clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@751d3241[object: org.codehaus.groovy.ast.expr.VariableExpression@76c7beb3[variable: params] property: ConstantExpression[clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@64337702[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2cf92cc7[org.codehaus.groovy.ast.expr.VariableExpression@30ea8c23[variable: c_r2]("=" at 369:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@7b139eab[org.codehaus.groovy.ast.expr.BooleanExpression@4e76dac ? org.codehaus.groovy.ast.expr.GStringExpression@611df6e3[strings: [ConstantExpression[--clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5f2f577[object: org.codehaus.groovy.ast.expr.VariableExpression@6273c5a4[variable: params] property: ConstantExpression[clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5d465e4b[expression:org.codehaus.groovy.ast.expr.BinaryExpression@53e211ee[org.codehaus.groovy.ast.expr.VariableExpression@41a90fa8[variable: tpc_r1]("=" at 370:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@3d8bbcdc[org.codehaus.groovy.ast.expr.BooleanExpression@52500920 ? org.codehaus.groovy.ast.expr.GStringExpression@117e0fe5[strings: [ConstantExpression[--three_prime_clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@18a3962d[object: org.codehaus.groovy.ast.expr.VariableExpression@78aea4b9[variable: params] property: ConstantExpression[three_prime_clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a65bb85[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4b85880b[org.codehaus.groovy.ast.expr.VariableExpression@4f936da8[variable: tpc_r2]("=" at 371:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@4215838f[org.codehaus.groovy.ast.expr.BooleanExpression@452ba1db ? org.codehaus.groovy.ast.expr.GStringExpression@2289aca5[strings: [ConstantExpression[--three_prime_clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76a36b71[object: org.codehaus.groovy.ast.expr.VariableExpression@184497d1[variable: params] property: ConstantExpression[three_prime_clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.IfStatement@f9d87b] }]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@6ffab045[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bf22f18[ConstantExpression[trim_galore], org.codehaus.groovy.ast.expr.ClosureExpression@267f474e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a7471ce[org.codehaus.groovy.ast.stmt.ExpressionStatement@28276e50[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62e70ea3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3efe7086[org.codehaus.groovy.ast.expr.MapExpression@675d8c96[org.codehaus.groovy.ast.expr.MapEntryExpression@741b3bc3(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2ed3b1f5[strings: [ConstantExpression[], ConstantExpression[/trim_galore]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@63648ee9[object: org.codehaus.groovy.ast.expr.VariableExpression@68d6972f[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@45be7cd5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7651218e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3185fa6b[org.codehaus.groovy.ast.expr.ClosureExpression@6d366c9b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5b58ed3c[org.codehaus.groovy.ast.stmt.ExpressionStatement@24faea88[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3a320ade[org.codehaus.groovy.ast.expr.BooleanExpression@64beebb7 ? org.codehaus.groovy.ast.expr.PropertyExpression@7813cb11[object: org.codehaus.groovy.ast.expr.VariableExpression@bcec031[variable: params] property: ConstantExpression[trim_galore_cpus]] : ConstantExpression[2]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21005f6c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@32f0fba8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@545de5a4[org.codehaus.groovy.ast.expr.ClosureExpression@29ef6856[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ab7a938[org.codehaus.groovy.ast.stmt.ExpressionStatement@3faf2e7d[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4648ce9[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@569bf9eb[org.codehaus.groovy.ast.expr.BooleanExpression@61526469 ? org.codehaus.groovy.ast.expr.PropertyExpression@274872f8[object: org.codehaus.groovy.ast.expr.VariableExpression@76ba13c[variable: params] property: ConstantExpression[trim_galore_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@eb6449b[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 355:50:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7c351808[object: org.codehaus.groovy.ast.expr.VariableExpression@180e6ac4[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42b64ab8[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7e985ce9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2a39fe6a[org.codehaus.groovy.ast.expr.ClosureExpression@410ae9a3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@319988b0[org.codehaus.groovy.ast.stmt.ExpressionStatement@d5ae57e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@68759011[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7e242b4d[org.codehaus.groovy.ast.expr.BooleanExpression@305f031 ? org.codehaus.groovy.ast.expr.PropertyExpression@592e843a[object: org.codehaus.groovy.ast.expr.VariableExpression@1d1f7216[variable: params] property: ConstantExpression[trim_galore_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@423e4cbb[object: ConstantExpression[8] property: ConstantExpression[h]]]("*" at 356:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6e16b8b5[object: org.codehaus.groovy.ast.expr.VariableExpression@43b4fe19[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25ddbbbb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1536602f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4ebea12c[org.codehaus.groovy.ast.expr.ClosureExpression@2a1edad4[]{ org.codehaus.groovy.ast.stmt.BlockStatement@6256ac4f[org.codehaus.groovy.ast.stmt.ExpressionStatement@44c79f32[expression:org.codehaus.groovy.ast.expr.TernaryExpression@7fcbe147[org.codehaus.groovy.ast.expr.BooleanExpression@235f4c10 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@743cb8e0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c7a975a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2c1b9e4b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@757d6814[org.codehaus.groovy.ast.expr.MethodCallExpression@649725e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3c0fae6c[org.codehaus.groovy.ast.expr.VariableExpression@4c168660[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@52b56a3e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@fd0e5b6[org.codehaus.groovy.ast.expr.VariableExpression@4eed46ee[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b0fcd5[org.codehaus.groovy.ast.expr.VariableExpression@4fad94a7[variable: read_files_trimming]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@475835b1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6326d182[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5241cf67[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@716a7124[ConstantExpression[*fq.gz]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@77192705[org.codehaus.groovy.ast.expr.VariableExpression@226642a5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7e809b79[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5cc126dc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@625e134e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72bd06ca[ConstantExpression[*trimming_report.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@89c10b7[org.codehaus.groovy.ast.expr.VariableExpression@5dbe30be[variable: trimgalore_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4fe89c24[expression:org.codehaus.groovy.ast.expr.BinaryExpression@55795845[org.codehaus.groovy.ast.expr.VariableExpression@3d08f3f5[variable: single]("=" at 367:12:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@119f1f2a[org.codehaus.groovy.ast.expr.VariableExpression@1a1da881[variable: reads]("instanceof" at 367:20:  "instanceof" )org.codehaus.groovy.ast.expr.ClassExpression@5b970f7[type: Path]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7fd4acee[expression:org.codehaus.groovy.ast.expr.BinaryExpression@165b8a71[org.codehaus.groovy.ast.expr.VariableExpression@6175619b[variable: c_r1]("=" at 368:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@2f058b8a[org.codehaus.groovy.ast.expr.BooleanExpression@756cf158 ? org.codehaus.groovy.ast.expr.GStringExpression@3f2ef586[strings: [ConstantExpression[--clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@751d3241[object: org.codehaus.groovy.ast.expr.VariableExpression@76c7beb3[variable: params] property: ConstantExpression[clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@64337702[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2cf92cc7[org.codehaus.groovy.ast.expr.VariableExpression@30ea8c23[variable: c_r2]("=" at 369:10:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@7b139eab[org.codehaus.groovy.ast.expr.BooleanExpression@4e76dac ? org.codehaus.groovy.ast.expr.GStringExpression@611df6e3[strings: [ConstantExpression[--clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5f2f577[object: org.codehaus.groovy.ast.expr.VariableExpression@6273c5a4[variable: params] property: ConstantExpression[clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5d465e4b[expression:org.codehaus.groovy.ast.expr.BinaryExpression@53e211ee[org.codehaus.groovy.ast.expr.VariableExpression@41a90fa8[variable: tpc_r1]("=" at 370:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@3d8bbcdc[org.codehaus.groovy.ast.expr.BooleanExpression@52500920 ? org.codehaus.groovy.ast.expr.GStringExpression@117e0fe5[strings: [ConstantExpression[--three_prime_clip_r1 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@18a3962d[object: org.codehaus.groovy.ast.expr.VariableExpression@78aea4b9[variable: params] property: ConstantExpression[three_prime_clip_r1]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a65bb85[expression:org.codehaus.groovy.ast.expr.BinaryExpression@4b85880b[org.codehaus.groovy.ast.expr.VariableExpression@4f936da8[variable: tpc_r2]("=" at 371:12:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@4215838f[org.codehaus.groovy.ast.expr.BooleanExpression@452ba1db ? org.codehaus.groovy.ast.expr.GStringExpression@2289aca5[strings: [ConstantExpression[--three_prime_clip_r2 ], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76a36b71[object: org.codehaus.groovy.ast.expr.VariableExpression@184497d1[variable: params] property: ConstantExpression[three_prime_clip_r2]]]] : ConstantExpression[]]]], org.codehaus.groovy.ast.stmt.IfStatement@f9d87b] }]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@c7a975a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2c1b9e4b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@757d6814[org.codehaus.groovy.ast.expr.MethodCallExpression@649725e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3c0fae6c[org.codehaus.groovy.ast.expr.VariableExpression@4c168660[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@52b56a3e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@fd0e5b6[org.codehaus.groovy.ast.expr.VariableExpression@4eed46ee[variable: reads]]]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b0fcd5[org.codehaus.groovy.ast.expr.VariableExpression@4fad94a7[variable: read_files_trimming]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2c1b9e4b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@757d6814[org.codehaus.groovy.ast.expr.MethodCallExpression@649725e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[val] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3c0fae6c[org.codehaus.groovy.ast.expr.VariableExpression@4c168660[variable: name]]], org.codehaus.groovy.ast.expr.MethodCallExpression@52b56a3e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@fd0e5b6[org.codehaus.groovy.ast.expr.VariableExpression@4eed46ee[variable: reads]]]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: set
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6326d182[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5241cf67[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@716a7124[ConstantExpression[*fq.gz]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@77192705[org.codehaus.groovy.ast.expr.VariableExpression@226642a5[variable: trimmed_reads]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5241cf67[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@716a7124[ConstantExpression[*fq.gz]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5cc126dc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@625e134e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72bd06ca[ConstantExpression[*trimming_report.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@89c10b7[org.codehaus.groovy.ast.expr.VariableExpression@5dbe30be[variable: trimgalore_results]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@625e134e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72bd06ca[ConstantExpression[*trimming_report.txt]]]
Nov-14 16:09:26.607 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.610 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@26fb628[org.codehaus.groovy.ast.expr.MethodCallExpression@3e2943ab[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[star] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@70dd7e15[org.codehaus.groovy.ast.expr.ClosureExpression@4a9f80d3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@35beb15e[org.codehaus.groovy.ast.stmt.ExpressionStatement@41fe9859[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ac86ba5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c67e137[org.codehaus.groovy.ast.expr.GStringExpression@2c9399a4[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@191ae03f[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@9635fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@53ab0286[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@63c5efee[org.codehaus.groovy.ast.expr.MapExpression@2d10e0b1[org.codehaus.groovy.ast.expr.MapEntryExpression@1c98290c(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@172ca72b[strings: [ConstantExpression[], ConstantExpression[/STAR]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5bda80bf[object: org.codehaus.groovy.ast.expr.VariableExpression@71e5f61d[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ce86164[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5e8f9e2d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51df223b[org.codehaus.groovy.ast.expr.ClosureExpression@fd46303[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60d8c0dc[org.codehaus.groovy.ast.stmt.ExpressionStatement@4204541c[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6a62689d[org.codehaus.groovy.ast.expr.BooleanExpression@4602c2a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@60fa3495[object: org.codehaus.groovy.ast.expr.VariableExpression@3e2822[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79e18e38[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29a60c27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1849db1a[org.codehaus.groovy.ast.expr.ClosureExpression@69c79f09[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1ca25c47[org.codehaus.groovy.ast.stmt.ExpressionStatement@5fcacc0[expression:org.codehaus.groovy.ast.expr.BinaryExpression@533b266e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6d1d4d7[org.codehaus.groovy.ast.expr.BooleanExpression@89ff02e ? org.codehaus.groovy.ast.expr.PropertyExpression@6865c751[object: org.codehaus.groovy.ast.expr.VariableExpression@62679465[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@6a988392[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 411:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1d71006f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b6813df[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5f2606b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2b58f754[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3ebff828[org.codehaus.groovy.ast.expr.ClosureExpression@2552f2cb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@33352f32[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f3b9c57[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1e044120[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2cf23c81[org.codehaus.groovy.ast.expr.BooleanExpression@3624da92 ? org.codehaus.groovy.ast.expr.PropertyExpression@35fe2125[object: org.codehaus.groovy.ast.expr.VariableExpression@94f6bfb[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@34645867[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 412:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2484f433[object: org.codehaus.groovy.ast.expr.VariableExpression@60b71e8f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1255b1d1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@464649c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c22d4f[org.codehaus.groovy.ast.expr.ClosureExpression@5f59185e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60bdf15d[org.codehaus.groovy.ast.stmt.ExpressionStatement@47da3952[expression:org.codehaus.groovy.ast.expr.TernaryExpression@51e4ccb3[org.codehaus.groovy.ast.expr.BooleanExpression@46e8a539 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@495083a0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5fd62371[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28a0fd6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2b62442c[org.codehaus.groovy.ast.expr.VariableExpression@66629f63[variable: star_index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@841e575[org.codehaus.groovy.ast.expr.VariableExpression@27a5328c[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1e5f4170[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c345c5f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6b5966e1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@65e61854[org.codehaus.groovy.ast.expr.VariableExpression@1568159[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4fcee388[org.codehaus.groovy.ast.expr.VariableExpression@6f80fafe[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3af17be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f9879ac[object: org.codehaus.groovy.ast.expr.MethodCallExpression@37f21974[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5f4d427e[org.codehaus.groovy.ast.expr.VariableExpression@6e521c1e[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@224b4d61[org.codehaus.groovy.ast.expr.VariableExpression@5d5d9e5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@303e3593[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4ef27d66[object: org.codehaus.groovy.ast.expr.MethodCallExpression@362a019c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1d9bec4d[org.codehaus.groovy.ast.expr.MethodCallExpression@5c48c0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c8f62[ConstantExpression[*Log.final.out]]], org.codehaus.groovy.ast.expr.MethodCallExpression@674c583e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25f7391e[ConstantExpression[*.bam]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f23a3a0[org.codehaus.groovy.ast.expr.VariableExpression@5ab14cb9[variable: star_aligned]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5fb97279[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@439a8f59[object: org.codehaus.groovy.ast.expr.MethodCallExpression@61861a29[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31024624[ConstantExpression[*.out]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25bcd0c7[org.codehaus.groovy.ast.expr.VariableExpression@32cb636e[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63cd604c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40dd3977[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a4e343[ConstantExpression[*SJ.out.tab]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a1d204a[expression:org.codehaus.groovy.ast.expr.GStringExpression@62dae245[strings: [ConstantExpression[
        #Getting STAR prefix
        f=(], ConstantExpression[);f=${f[0]};f=${f%.gz};f=${f%.fastq};f=${f%.fq};f=${f%_val_1};f=${f%_trimmed};f=${f%_1};f=${f%_R1}
        STAR --genomeDir ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --readFilesIn ], ConstantExpression[  \
            --runThreadN ], ConstantExpression[ \
            --twopassMode Basic \
            --outWigType bedGraph \
            --outSAMtype BAM SortedByCoordinate \
            --readFilesCommand zcat \
            --outFileNamePrefix $f
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4b6579e8[variable: reads], org.codehaus.groovy.ast.expr.VariableExpression@6fff253c[variable: star_index], org.codehaus.groovy.ast.expr.VariableExpression@6c6357f9[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@591e58fa[variable: reads], org.codehaus.groovy.ast.expr.PropertyExpression@3954d008[object: org.codehaus.groovy.ast.expr.VariableExpression@2f94c4db[variable: task] property: ConstantExpression[cpus]]]]]] }]]]
Nov-14 16:09:26.611 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: star with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@70dd7e15[org.codehaus.groovy.ast.expr.ClosureExpression@4a9f80d3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@35beb15e[org.codehaus.groovy.ast.stmt.ExpressionStatement@41fe9859[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ac86ba5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c67e137[org.codehaus.groovy.ast.expr.GStringExpression@2c9399a4[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@191ae03f[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@9635fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@53ab0286[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@63c5efee[org.codehaus.groovy.ast.expr.MapExpression@2d10e0b1[org.codehaus.groovy.ast.expr.MapEntryExpression@1c98290c(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@172ca72b[strings: [ConstantExpression[], ConstantExpression[/STAR]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5bda80bf[object: org.codehaus.groovy.ast.expr.VariableExpression@71e5f61d[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ce86164[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5e8f9e2d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51df223b[org.codehaus.groovy.ast.expr.ClosureExpression@fd46303[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60d8c0dc[org.codehaus.groovy.ast.stmt.ExpressionStatement@4204541c[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6a62689d[org.codehaus.groovy.ast.expr.BooleanExpression@4602c2a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@60fa3495[object: org.codehaus.groovy.ast.expr.VariableExpression@3e2822[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79e18e38[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29a60c27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1849db1a[org.codehaus.groovy.ast.expr.ClosureExpression@69c79f09[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1ca25c47[org.codehaus.groovy.ast.stmt.ExpressionStatement@5fcacc0[expression:org.codehaus.groovy.ast.expr.BinaryExpression@533b266e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6d1d4d7[org.codehaus.groovy.ast.expr.BooleanExpression@89ff02e ? org.codehaus.groovy.ast.expr.PropertyExpression@6865c751[object: org.codehaus.groovy.ast.expr.VariableExpression@62679465[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@6a988392[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 411:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1d71006f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b6813df[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5f2606b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2b58f754[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3ebff828[org.codehaus.groovy.ast.expr.ClosureExpression@2552f2cb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@33352f32[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f3b9c57[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1e044120[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2cf23c81[org.codehaus.groovy.ast.expr.BooleanExpression@3624da92 ? org.codehaus.groovy.ast.expr.PropertyExpression@35fe2125[object: org.codehaus.groovy.ast.expr.VariableExpression@94f6bfb[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@34645867[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 412:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2484f433[object: org.codehaus.groovy.ast.expr.VariableExpression@60b71e8f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1255b1d1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@464649c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c22d4f[org.codehaus.groovy.ast.expr.ClosureExpression@5f59185e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60bdf15d[org.codehaus.groovy.ast.stmt.ExpressionStatement@47da3952[expression:org.codehaus.groovy.ast.expr.TernaryExpression@51e4ccb3[org.codehaus.groovy.ast.expr.BooleanExpression@46e8a539 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@495083a0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5fd62371[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28a0fd6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2b62442c[org.codehaus.groovy.ast.expr.VariableExpression@66629f63[variable: star_index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@841e575[org.codehaus.groovy.ast.expr.VariableExpression@27a5328c[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1e5f4170[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c345c5f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6b5966e1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@65e61854[org.codehaus.groovy.ast.expr.VariableExpression@1568159[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4fcee388[org.codehaus.groovy.ast.expr.VariableExpression@6f80fafe[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3af17be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f9879ac[object: org.codehaus.groovy.ast.expr.MethodCallExpression@37f21974[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5f4d427e[org.codehaus.groovy.ast.expr.VariableExpression@6e521c1e[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@224b4d61[org.codehaus.groovy.ast.expr.VariableExpression@5d5d9e5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@303e3593[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4ef27d66[object: org.codehaus.groovy.ast.expr.MethodCallExpression@362a019c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1d9bec4d[org.codehaus.groovy.ast.expr.MethodCallExpression@5c48c0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c8f62[ConstantExpression[*Log.final.out]]], org.codehaus.groovy.ast.expr.MethodCallExpression@674c583e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25f7391e[ConstantExpression[*.bam]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f23a3a0[org.codehaus.groovy.ast.expr.VariableExpression@5ab14cb9[variable: star_aligned]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5fb97279[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@439a8f59[object: org.codehaus.groovy.ast.expr.MethodCallExpression@61861a29[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31024624[ConstantExpression[*.out]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25bcd0c7[org.codehaus.groovy.ast.expr.VariableExpression@32cb636e[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63cd604c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40dd3977[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a4e343[ConstantExpression[*SJ.out.tab]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a1d204a[expression:org.codehaus.groovy.ast.expr.GStringExpression@62dae245[strings: [ConstantExpression[
        #Getting STAR prefix
        f=(], ConstantExpression[);f=${f[0]};f=${f%.gz};f=${f%.fastq};f=${f%.fq};f=${f%_val_1};f=${f%_trimmed};f=${f%_1};f=${f%_R1}
        STAR --genomeDir ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --readFilesIn ], ConstantExpression[  \
            --runThreadN ], ConstantExpression[ \
            --twopassMode Basic \
            --outWigType bedGraph \
            --outSAMtype BAM SortedByCoordinate \
            --readFilesCommand zcat \
            --outFileNamePrefix $f
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4b6579e8[variable: reads], org.codehaus.groovy.ast.expr.VariableExpression@6fff253c[variable: star_index], org.codehaus.groovy.ast.expr.VariableExpression@6c6357f9[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@591e58fa[variable: reads], org.codehaus.groovy.ast.expr.PropertyExpression@3954d008[object: org.codehaus.groovy.ast.expr.VariableExpression@2f94c4db[variable: task] property: ConstantExpression[cpus]]]]]] }]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@593e824f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@70dd7e15[ConstantExpression[star], org.codehaus.groovy.ast.expr.ClosureExpression@4a9f80d3[]{ org.codehaus.groovy.ast.stmt.BlockStatement@35beb15e[org.codehaus.groovy.ast.stmt.ExpressionStatement@41fe9859[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ac86ba5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c67e137[org.codehaus.groovy.ast.expr.GStringExpression@2c9399a4[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@191ae03f[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@9635fa[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@53ab0286[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@63c5efee[org.codehaus.groovy.ast.expr.MapExpression@2d10e0b1[org.codehaus.groovy.ast.expr.MapEntryExpression@1c98290c(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@172ca72b[strings: [ConstantExpression[], ConstantExpression[/STAR]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@5bda80bf[object: org.codehaus.groovy.ast.expr.VariableExpression@71e5f61d[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ce86164[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5e8f9e2d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51df223b[org.codehaus.groovy.ast.expr.ClosureExpression@fd46303[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60d8c0dc[org.codehaus.groovy.ast.stmt.ExpressionStatement@4204541c[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6a62689d[org.codehaus.groovy.ast.expr.BooleanExpression@4602c2a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@60fa3495[object: org.codehaus.groovy.ast.expr.VariableExpression@3e2822[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79e18e38[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29a60c27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1849db1a[org.codehaus.groovy.ast.expr.ClosureExpression@69c79f09[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1ca25c47[org.codehaus.groovy.ast.stmt.ExpressionStatement@5fcacc0[expression:org.codehaus.groovy.ast.expr.BinaryExpression@533b266e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6d1d4d7[org.codehaus.groovy.ast.expr.BooleanExpression@89ff02e ? org.codehaus.groovy.ast.expr.PropertyExpression@6865c751[object: org.codehaus.groovy.ast.expr.VariableExpression@62679465[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@6a988392[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 411:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1d71006f[object: org.codehaus.groovy.ast.expr.VariableExpression@5b6813df[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5f2606b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2b58f754[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3ebff828[org.codehaus.groovy.ast.expr.ClosureExpression@2552f2cb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@33352f32[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f3b9c57[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1e044120[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@2cf23c81[org.codehaus.groovy.ast.expr.BooleanExpression@3624da92 ? org.codehaus.groovy.ast.expr.PropertyExpression@35fe2125[object: org.codehaus.groovy.ast.expr.VariableExpression@94f6bfb[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@34645867[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 412:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2484f433[object: org.codehaus.groovy.ast.expr.VariableExpression@60b71e8f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1255b1d1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@464649c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7c22d4f[org.codehaus.groovy.ast.expr.ClosureExpression@5f59185e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@60bdf15d[org.codehaus.groovy.ast.stmt.ExpressionStatement@47da3952[expression:org.codehaus.groovy.ast.expr.TernaryExpression@51e4ccb3[org.codehaus.groovy.ast.expr.BooleanExpression@46e8a539 ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@495083a0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5fd62371[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28a0fd6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2b62442c[org.codehaus.groovy.ast.expr.VariableExpression@66629f63[variable: star_index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@841e575[org.codehaus.groovy.ast.expr.VariableExpression@27a5328c[variable: star_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1e5f4170[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6c345c5f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6b5966e1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@65e61854[org.codehaus.groovy.ast.expr.VariableExpression@1568159[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4fcee388[org.codehaus.groovy.ast.expr.VariableExpression@6f80fafe[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3af17be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f9879ac[object: org.codehaus.groovy.ast.expr.MethodCallExpression@37f21974[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5f4d427e[org.codehaus.groovy.ast.expr.VariableExpression@6e521c1e[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@224b4d61[org.codehaus.groovy.ast.expr.VariableExpression@5d5d9e5[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@303e3593[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4ef27d66[object: org.codehaus.groovy.ast.expr.MethodCallExpression@362a019c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1d9bec4d[org.codehaus.groovy.ast.expr.MethodCallExpression@5c48c0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c8f62[ConstantExpression[*Log.final.out]]], org.codehaus.groovy.ast.expr.MethodCallExpression@674c583e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25f7391e[ConstantExpression[*.bam]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f23a3a0[org.codehaus.groovy.ast.expr.VariableExpression@5ab14cb9[variable: star_aligned]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5fb97279[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@439a8f59[object: org.codehaus.groovy.ast.expr.MethodCallExpression@61861a29[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31024624[ConstantExpression[*.out]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25bcd0c7[org.codehaus.groovy.ast.expr.VariableExpression@32cb636e[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@63cd604c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@40dd3977[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a4e343[ConstantExpression[*SJ.out.tab]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a1d204a[expression:org.codehaus.groovy.ast.expr.GStringExpression@62dae245[strings: [ConstantExpression[
        #Getting STAR prefix
        f=(], ConstantExpression[);f=${f[0]};f=${f%.gz};f=${f%.fastq};f=${f%.fq};f=${f%_val_1};f=${f%_trimmed};f=${f%_1};f=${f%_R1}
        STAR --genomeDir ], ConstantExpression[ \
            --sjdbGTFfile ], ConstantExpression[ \
            --readFilesIn ], ConstantExpression[  \
            --runThreadN ], ConstantExpression[ \
            --twopassMode Basic \
            --outWigType bedGraph \
            --outSAMtype BAM SortedByCoordinate \
            --readFilesCommand zcat \
            --outFileNamePrefix $f
        ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@4b6579e8[variable: reads], org.codehaus.groovy.ast.expr.VariableExpression@6fff253c[variable: star_index], org.codehaus.groovy.ast.expr.VariableExpression@6c6357f9[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@591e58fa[variable: reads], org.codehaus.groovy.ast.expr.PropertyExpression@3954d008[object: org.codehaus.groovy.ast.expr.VariableExpression@2f94c4db[variable: task] property: ConstantExpression[cpus]]]]]] }]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5fd62371[object: org.codehaus.groovy.ast.expr.MethodCallExpression@28a0fd6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2b62442c[org.codehaus.groovy.ast.expr.VariableExpression@66629f63[variable: star_index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@841e575[org.codehaus.groovy.ast.expr.VariableExpression@27a5328c[variable: star_index]]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@28a0fd6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2b62442c[org.codehaus.groovy.ast.expr.VariableExpression@66629f63[variable: star_index]]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6c345c5f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@6b5966e1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@65e61854[org.codehaus.groovy.ast.expr.VariableExpression@1568159[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4fcee388[org.codehaus.groovy.ast.expr.VariableExpression@6f80fafe[variable: gtf]]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6b5966e1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@65e61854[org.codehaus.groovy.ast.expr.VariableExpression@1568159[variable: gtf]]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@f9879ac[object: org.codehaus.groovy.ast.expr.MethodCallExpression@37f21974[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5f4d427e[org.codehaus.groovy.ast.expr.VariableExpression@6e521c1e[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@224b4d61[org.codehaus.groovy.ast.expr.VariableExpression@5d5d9e5[variable: trimmed_reads]]]
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.612 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@37f21974[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5f4d427e[org.codehaus.groovy.ast.expr.VariableExpression@6e521c1e[variable: reads]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4ef27d66[object: org.codehaus.groovy.ast.expr.MethodCallExpression@362a019c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1d9bec4d[org.codehaus.groovy.ast.expr.MethodCallExpression@5c48c0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c8f62[ConstantExpression[*Log.final.out]]], org.codehaus.groovy.ast.expr.MethodCallExpression@674c583e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25f7391e[ConstantExpression[*.bam]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f23a3a0[org.codehaus.groovy.ast.expr.VariableExpression@5ab14cb9[variable: star_aligned]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@362a019c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[set] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1d9bec4d[org.codehaus.groovy.ast.expr.MethodCallExpression@5c48c0c0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@10c8f62[ConstantExpression[*Log.final.out]]], org.codehaus.groovy.ast.expr.MethodCallExpression@674c583e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25f7391e[ConstantExpression[*.bam]]]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: set
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@439a8f59[object: org.codehaus.groovy.ast.expr.MethodCallExpression@61861a29[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31024624[ConstantExpression[*.out]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@25bcd0c7[org.codehaus.groovy.ast.expr.VariableExpression@32cb636e[variable: alignment_logs]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@61861a29[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31024624[ConstantExpression[*.out]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@40dd3977[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a4e343[ConstantExpression[*SJ.out.tab]]]
Nov-14 16:09:26.613 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.616 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@72ccd81a[org.codehaus.groovy.ast.expr.MethodCallExpression@6d8792db[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[hisat2] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64bc21ac[org.codehaus.groovy.ast.expr.ClosureExpression@493dfb8e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5d25e6bb[org.codehaus.groovy.ast.stmt.ExpressionStatement@ce5a68e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9d157ff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f162cc0[org.codehaus.groovy.ast.expr.GStringExpression@5df417a7[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7c041b41[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7f69d591[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@61078690[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1cb3ec38[org.codehaus.groovy.ast.expr.MapExpression@403132fc[org.codehaus.groovy.ast.expr.MapEntryExpression@71c5b236(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2cab9998[strings: [ConstantExpression[], ConstantExpression[/HISAT2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2f7a7219[object: org.codehaus.groovy.ast.expr.VariableExpression@669513d8[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a1d593e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4a8a60bc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@361c294e[org.codehaus.groovy.ast.expr.ClosureExpression@7859e786[]{ org.codehaus.groovy.ast.stmt.BlockStatement@285d851a[org.codehaus.groovy.ast.stmt.ExpressionStatement@314b8f2d[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@664a9613[org.codehaus.groovy.ast.expr.BooleanExpression@5118388b ? org.codehaus.groovy.ast.expr.PropertyExpression@15a902e7[object: org.codehaus.groovy.ast.expr.VariableExpression@7876d598[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a3e3e8b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5af28b27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71104a4[org.codehaus.groovy.ast.expr.ClosureExpression@4985cbcb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72f46e16[org.codehaus.groovy.ast.stmt.ExpressionStatement@3c9168dc[expression:org.codehaus.groovy.ast.expr.BinaryExpression@332a7fce[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@549621f3[org.codehaus.groovy.ast.expr.BooleanExpression@54361a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@32232e55[object: org.codehaus.groovy.ast.expr.VariableExpression@5217f3d0[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@37ebc9d8[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 457:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@293bb8a5[object: org.codehaus.groovy.ast.expr.VariableExpression@2416a51[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6fa590ba[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e9319f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72e34f77[org.codehaus.groovy.ast.expr.ClosureExpression@7bf9b098[]{ org.codehaus.groovy.ast.stmt.BlockStatement@389adf1d[org.codehaus.groovy.ast.stmt.ExpressionStatement@77307458[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1fc0053e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@290b1b2e[org.codehaus.groovy.ast.expr.BooleanExpression@47874b25 ? org.codehaus.groovy.ast.expr.PropertyExpression@33617539[object: org.codehaus.groovy.ast.expr.VariableExpression@2c177f9e[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5db4c359[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 458:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@209775a9[object: org.codehaus.groovy.ast.expr.VariableExpression@18e7143f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f9b7332[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@74cec793[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6fefce9e[org.codehaus.groovy.ast.expr.ClosureExpression@4f8969b0[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bdf8190[org.codehaus.groovy.ast.stmt.ExpressionStatement@192f2f27[expression:org.codehaus.groovy.ast.expr.TernaryExpression@8a589a2[org.codehaus.groovy.ast.expr.BooleanExpression@c65a5ef ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6b5176f2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@b672aa8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fab4aff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ec0c838[org.codehaus.groovy.ast.expr.VariableExpression@6e46d9f4[variable: index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5cc69cfe[org.codehaus.groovy.ast.expr.VariableExpression@29cfd92b[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21c64522[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7997b197[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11dee337[org.codehaus.groovy.ast.expr.VariableExpression@460f76a6[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@55f3c410[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11acdc30[object: org.codehaus.groovy.ast.expr.MethodCallExpression@770d4269[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a8ab068[org.codehaus.groovy.ast.expr.VariableExpression@1922e6d[variable: alignment_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76a82f33[org.codehaus.groovy.ast.expr.VariableExpression@6bab2585[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@74bdc168[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@644c78d4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@532a02d9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@611f8234[org.codehaus.groovy.ast.expr.VariableExpression@7bb3a9fe[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cbee484[org.codehaus.groovy.ast.expr.VariableExpression@7f811d00[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62923ee6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4089713[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f19c9d2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7807ac2c[ConstantExpression[*.bam]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@b91d8c4[org.codehaus.groovy.ast.expr.VariableExpression@4b6166aa[variable: bam_count], org.codehaus.groovy.ast.expr.VariableExpression@a77614d[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@4fd4cae3[variable: bam_preseq], org.codehaus.groovy.ast.expr.VariableExpression@4a067c25[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.VariableExpression@a1217f9[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@3bde62ff[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@523424b5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2baa8d82[object: org.codehaus.groovy.ast.expr.MethodCallExpression@319dead1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@791cbf87[ConstantExpression[*.hisat2_log.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a7e2d9d[org.codehaus.groovy.ast.expr.VariableExpression@754777cd[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2b52c0d6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@372ea2bc[org.codehaus.groovy.ast.expr.VariableExpression@4cc76301[variable: index_base]("=" at 472:20:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@2f08c4b[org.codehaus.groovy.ast.expr.VariableExpression@3f19b8b3[variable: index]("-" at 472:28:  "-" )org.codehaus.groovy.ast.expr.BitwiseNegationExpression@7de0c6ae]]], org.codehaus.groovy.ast.stmt.IfStatement@a486d78] }]]]
Nov-14 16:09:26.616 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: hisat2 with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@64bc21ac[org.codehaus.groovy.ast.expr.ClosureExpression@493dfb8e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5d25e6bb[org.codehaus.groovy.ast.stmt.ExpressionStatement@ce5a68e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9d157ff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f162cc0[org.codehaus.groovy.ast.expr.GStringExpression@5df417a7[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7c041b41[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7f69d591[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@61078690[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1cb3ec38[org.codehaus.groovy.ast.expr.MapExpression@403132fc[org.codehaus.groovy.ast.expr.MapEntryExpression@71c5b236(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2cab9998[strings: [ConstantExpression[], ConstantExpression[/HISAT2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2f7a7219[object: org.codehaus.groovy.ast.expr.VariableExpression@669513d8[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a1d593e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4a8a60bc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@361c294e[org.codehaus.groovy.ast.expr.ClosureExpression@7859e786[]{ org.codehaus.groovy.ast.stmt.BlockStatement@285d851a[org.codehaus.groovy.ast.stmt.ExpressionStatement@314b8f2d[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@664a9613[org.codehaus.groovy.ast.expr.BooleanExpression@5118388b ? org.codehaus.groovy.ast.expr.PropertyExpression@15a902e7[object: org.codehaus.groovy.ast.expr.VariableExpression@7876d598[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a3e3e8b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5af28b27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71104a4[org.codehaus.groovy.ast.expr.ClosureExpression@4985cbcb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72f46e16[org.codehaus.groovy.ast.stmt.ExpressionStatement@3c9168dc[expression:org.codehaus.groovy.ast.expr.BinaryExpression@332a7fce[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@549621f3[org.codehaus.groovy.ast.expr.BooleanExpression@54361a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@32232e55[object: org.codehaus.groovy.ast.expr.VariableExpression@5217f3d0[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@37ebc9d8[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 457:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@293bb8a5[object: org.codehaus.groovy.ast.expr.VariableExpression@2416a51[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6fa590ba[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e9319f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72e34f77[org.codehaus.groovy.ast.expr.ClosureExpression@7bf9b098[]{ org.codehaus.groovy.ast.stmt.BlockStatement@389adf1d[org.codehaus.groovy.ast.stmt.ExpressionStatement@77307458[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1fc0053e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@290b1b2e[org.codehaus.groovy.ast.expr.BooleanExpression@47874b25 ? org.codehaus.groovy.ast.expr.PropertyExpression@33617539[object: org.codehaus.groovy.ast.expr.VariableExpression@2c177f9e[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5db4c359[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 458:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@209775a9[object: org.codehaus.groovy.ast.expr.VariableExpression@18e7143f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f9b7332[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@74cec793[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6fefce9e[org.codehaus.groovy.ast.expr.ClosureExpression@4f8969b0[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bdf8190[org.codehaus.groovy.ast.stmt.ExpressionStatement@192f2f27[expression:org.codehaus.groovy.ast.expr.TernaryExpression@8a589a2[org.codehaus.groovy.ast.expr.BooleanExpression@c65a5ef ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6b5176f2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@b672aa8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fab4aff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ec0c838[org.codehaus.groovy.ast.expr.VariableExpression@6e46d9f4[variable: index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5cc69cfe[org.codehaus.groovy.ast.expr.VariableExpression@29cfd92b[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21c64522[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7997b197[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11dee337[org.codehaus.groovy.ast.expr.VariableExpression@460f76a6[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@55f3c410[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11acdc30[object: org.codehaus.groovy.ast.expr.MethodCallExpression@770d4269[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a8ab068[org.codehaus.groovy.ast.expr.VariableExpression@1922e6d[variable: alignment_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76a82f33[org.codehaus.groovy.ast.expr.VariableExpression@6bab2585[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@74bdc168[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@644c78d4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@532a02d9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@611f8234[org.codehaus.groovy.ast.expr.VariableExpression@7bb3a9fe[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cbee484[org.codehaus.groovy.ast.expr.VariableExpression@7f811d00[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62923ee6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4089713[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f19c9d2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7807ac2c[ConstantExpression[*.bam]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@b91d8c4[org.codehaus.groovy.ast.expr.VariableExpression@4b6166aa[variable: bam_count], org.codehaus.groovy.ast.expr.VariableExpression@a77614d[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@4fd4cae3[variable: bam_preseq], org.codehaus.groovy.ast.expr.VariableExpression@4a067c25[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.VariableExpression@a1217f9[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@3bde62ff[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@523424b5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2baa8d82[object: org.codehaus.groovy.ast.expr.MethodCallExpression@319dead1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@791cbf87[ConstantExpression[*.hisat2_log.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a7e2d9d[org.codehaus.groovy.ast.expr.VariableExpression@754777cd[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2b52c0d6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@372ea2bc[org.codehaus.groovy.ast.expr.VariableExpression@4cc76301[variable: index_base]("=" at 472:20:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@2f08c4b[org.codehaus.groovy.ast.expr.VariableExpression@3f19b8b3[variable: index]("-" at 472:28:  "-" )org.codehaus.groovy.ast.expr.BitwiseNegationExpression@7de0c6ae]]], org.codehaus.groovy.ast.stmt.IfStatement@a486d78] }]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@cdc3aae[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64bc21ac[ConstantExpression[hisat2], org.codehaus.groovy.ast.expr.ClosureExpression@493dfb8e[]{ org.codehaus.groovy.ast.stmt.BlockStatement@5d25e6bb[org.codehaus.groovy.ast.stmt.ExpressionStatement@ce5a68e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9d157ff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f162cc0[org.codehaus.groovy.ast.expr.GStringExpression@5df417a7[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7c041b41[variable: reads]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7f69d591[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@61078690[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1cb3ec38[org.codehaus.groovy.ast.expr.MapExpression@403132fc[org.codehaus.groovy.ast.expr.MapEntryExpression@71c5b236(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@2cab9998[strings: [ConstantExpression[], ConstantExpression[/HISAT2]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2f7a7219[object: org.codehaus.groovy.ast.expr.VariableExpression@669513d8[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a1d593e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4a8a60bc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[cpus] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@361c294e[org.codehaus.groovy.ast.expr.ClosureExpression@7859e786[]{ org.codehaus.groovy.ast.stmt.BlockStatement@285d851a[org.codehaus.groovy.ast.stmt.ExpressionStatement@314b8f2d[expression:org.codehaus.groovy.ast.expr.ElvisOperatorExpression@664a9613[org.codehaus.groovy.ast.expr.BooleanExpression@5118388b ? org.codehaus.groovy.ast.expr.PropertyExpression@15a902e7[object: org.codehaus.groovy.ast.expr.VariableExpression@7876d598[variable: params] property: ConstantExpression[star_cpus]] : ConstantExpression[10]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4a3e3e8b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5af28b27[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71104a4[org.codehaus.groovy.ast.expr.ClosureExpression@4985cbcb[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72f46e16[org.codehaus.groovy.ast.stmt.ExpressionStatement@3c9168dc[expression:org.codehaus.groovy.ast.expr.BinaryExpression@332a7fce[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@549621f3[org.codehaus.groovy.ast.expr.BooleanExpression@54361a9 ? org.codehaus.groovy.ast.expr.PropertyExpression@32232e55[object: org.codehaus.groovy.ast.expr.VariableExpression@5217f3d0[variable: params] property: ConstantExpression[star_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@37ebc9d8[object: ConstantExpression[80] property: ConstantExpression[GB]]]("*" at 457:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@293bb8a5[object: org.codehaus.groovy.ast.expr.VariableExpression@2416a51[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6fa590ba[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e9319f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@72e34f77[org.codehaus.groovy.ast.expr.ClosureExpression@7bf9b098[]{ org.codehaus.groovy.ast.stmt.BlockStatement@389adf1d[org.codehaus.groovy.ast.stmt.ExpressionStatement@77307458[expression:org.codehaus.groovy.ast.expr.BinaryExpression@1fc0053e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@290b1b2e[org.codehaus.groovy.ast.expr.BooleanExpression@47874b25 ? org.codehaus.groovy.ast.expr.PropertyExpression@33617539[object: org.codehaus.groovy.ast.expr.VariableExpression@2c177f9e[variable: params] property: ConstantExpression[star_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5db4c359[object: ConstantExpression[5] property: ConstantExpression[h]]]("*" at 458:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@209775a9[object: org.codehaus.groovy.ast.expr.VariableExpression@18e7143f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@f9b7332[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@74cec793[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6fefce9e[org.codehaus.groovy.ast.expr.ClosureExpression@4f8969b0[]{ org.codehaus.groovy.ast.stmt.BlockStatement@1bdf8190[org.codehaus.groovy.ast.stmt.ExpressionStatement@192f2f27[expression:org.codehaus.groovy.ast.expr.TernaryExpression@8a589a2[org.codehaus.groovy.ast.expr.BooleanExpression@c65a5ef ? ConstantExpression[retry] : ConstantExpression[terminate]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6b5176f2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@b672aa8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fab4aff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ec0c838[org.codehaus.groovy.ast.expr.VariableExpression@6e46d9f4[variable: index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5cc69cfe[org.codehaus.groovy.ast.expr.VariableExpression@29cfd92b[variable: hisat2_index]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21c64522[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7997b197[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11dee337[org.codehaus.groovy.ast.expr.VariableExpression@460f76a6[variable: hs2_indices]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@55f3c410[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11acdc30[object: org.codehaus.groovy.ast.expr.MethodCallExpression@770d4269[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a8ab068[org.codehaus.groovy.ast.expr.VariableExpression@1922e6d[variable: alignment_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76a82f33[org.codehaus.groovy.ast.expr.VariableExpression@6bab2585[variable: alignment_splicesites]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@74bdc168[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@644c78d4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@532a02d9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@611f8234[org.codehaus.groovy.ast.expr.VariableExpression@7bb3a9fe[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cbee484[org.codehaus.groovy.ast.expr.VariableExpression@7f811d00[variable: trimmed_reads]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@62923ee6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4089713[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f19c9d2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7807ac2c[ConstantExpression[*.bam]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@b91d8c4[org.codehaus.groovy.ast.expr.VariableExpression@4b6166aa[variable: bam_count], org.codehaus.groovy.ast.expr.VariableExpression@a77614d[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@4fd4cae3[variable: bam_preseq], org.codehaus.groovy.ast.expr.VariableExpression@4a067c25[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.VariableExpression@a1217f9[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@3bde62ff[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@523424b5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2baa8d82[object: org.codehaus.groovy.ast.expr.MethodCallExpression@319dead1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@791cbf87[ConstantExpression[*.hisat2_log.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a7e2d9d[org.codehaus.groovy.ast.expr.VariableExpression@754777cd[variable: alignment_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2b52c0d6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@372ea2bc[org.codehaus.groovy.ast.expr.VariableExpression@4cc76301[variable: index_base]("=" at 472:20:  "=" )org.codehaus.groovy.ast.expr.BinaryExpression@2f08c4b[org.codehaus.groovy.ast.expr.VariableExpression@3f19b8b3[variable: index]("-" at 472:28:  "-" )org.codehaus.groovy.ast.expr.BitwiseNegationExpression@7de0c6ae]]], org.codehaus.groovy.ast.stmt.IfStatement@a486d78] }]]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@b672aa8[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fab4aff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ec0c838[org.codehaus.groovy.ast.expr.VariableExpression@6e46d9f4[variable: index]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5cc69cfe[org.codehaus.groovy.ast.expr.VariableExpression@29cfd92b[variable: hisat2_index]]]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2fab4aff[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@ec0c838[org.codehaus.groovy.ast.expr.VariableExpression@6e46d9f4[variable: index]]]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@7997b197[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11dee337[org.codehaus.groovy.ast.expr.VariableExpression@460f76a6[variable: hs2_indices]]]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@11acdc30[object: org.codehaus.groovy.ast.expr.MethodCallExpression@770d4269[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a8ab068[org.codehaus.groovy.ast.expr.VariableExpression@1922e6d[variable: alignment_splicesites]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@76a82f33[org.codehaus.groovy.ast.expr.VariableExpression@6bab2585[variable: alignment_splicesites]]]
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.617 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@770d4269[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a8ab068[org.codehaus.groovy.ast.expr.VariableExpression@1922e6d[variable: alignment_splicesites]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@644c78d4[object: org.codehaus.groovy.ast.expr.MethodCallExpression@532a02d9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@611f8234[org.codehaus.groovy.ast.expr.VariableExpression@7bb3a9fe[variable: reads]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cbee484[org.codehaus.groovy.ast.expr.VariableExpression@7f811d00[variable: trimmed_reads]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@532a02d9[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@611f8234[org.codehaus.groovy.ast.expr.VariableExpression@7bb3a9fe[variable: reads]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4089713[object: org.codehaus.groovy.ast.expr.MethodCallExpression@f19c9d2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7807ac2c[ConstantExpression[*.bam]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@b91d8c4[org.codehaus.groovy.ast.expr.VariableExpression@4b6166aa[variable: bam_count], org.codehaus.groovy.ast.expr.VariableExpression@a77614d[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@4fd4cae3[variable: bam_preseq], org.codehaus.groovy.ast.expr.VariableExpression@4a067c25[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.VariableExpression@a1217f9[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@3bde62ff[variable: bam_stringtieFPKM]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@f19c9d2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7807ac2c[ConstantExpression[*.bam]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2baa8d82[object: org.codehaus.groovy.ast.expr.MethodCallExpression@319dead1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@791cbf87[ConstantExpression[*.hisat2_log.txt]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a7e2d9d[org.codehaus.groovy.ast.expr.VariableExpression@754777cd[variable: alignment_logs]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@319dead1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@791cbf87[ConstantExpression[*.hisat2_log.txt]]]
Nov-14 16:09:26.618 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.624 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@7ef2d7a6[org.codehaus.groovy.ast.expr.MethodCallExpression@5dcbb60[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[rseqc] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4c36250e[org.codehaus.groovy.ast.expr.ClosureExpression@21526f6c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@49f5c307[org.codehaus.groovy.ast.stmt.ExpressionStatement@299266e2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5471388b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@66ea1466[org.codehaus.groovy.ast.expr.GStringExpression@1601e47[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@3bffddff[variable: bam_rseqc]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66971f6b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50687efb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@517bd097[org.codehaus.groovy.ast.expr.MapExpression@142eef62[org.codehaus.groovy.ast.expr.MapEntryExpression@4a9cc6cb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@5990e6c5[strings: [ConstantExpression[], ConstantExpression[/rseqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@56e07a08[object: org.codehaus.groovy.ast.expr.VariableExpression@35d6ca49[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1950e8a6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@47289387[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12cd9150[org.codehaus.groovy.ast.expr.ClosureExpression@114a85c2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@f415a95[org.codehaus.groovy.ast.stmt.ExpressionStatement@cf65451[expression:org.codehaus.groovy.ast.expr.BinaryExpression@724f138e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37eeec90[org.codehaus.groovy.ast.expr.BooleanExpression@32fe9d0a ? org.codehaus.groovy.ast.expr.PropertyExpression@c9413d8[object: org.codehaus.groovy.ast.expr.VariableExpression@64da2a7[variable: params] property: ConstantExpression[rseqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@46074492[object: ConstantExpression[32] property: ConstantExpression[GB]]]("*" at 512:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@d78795[object: org.codehaus.groovy.ast.expr.VariableExpression@2c715e84[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47428937[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b9d6699[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7caa550[org.codehaus.groovy.ast.expr.ClosureExpression@21694e53[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72b16078[org.codehaus.groovy.ast.stmt.ExpressionStatement@22c86919[expression:org.codehaus.groovy.ast.expr.BinaryExpression@70fab835[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1b0a7baf[org.codehaus.groovy.ast.expr.BooleanExpression@62417a16 ? org.codehaus.groovy.ast.expr.PropertyExpression@32057e6[object: org.codehaus.groovy.ast.expr.VariableExpression@26be6ca7[variable: params] property: ConstantExpression[rseqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6ea1bcdc[object: ConstantExpression[7] property: ConstantExpression[h]]]("*" at 513:39:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@759fad4[object: org.codehaus.groovy.ast.expr.VariableExpression@64712be[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@53499d85[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@30ed9c6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@782a4fff[org.codehaus.groovy.ast.expr.VariableExpression@46c670a6[variable: bam_rseqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@59fc684e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ae81e1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fd1731c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5ae76500[org.codehaus.groovy.ast.expr.VariableExpression@6063d80a[variable: bed12]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1133ec6e[org.codehaus.groovy.ast.expr.VariableExpression@355e34c7[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54709809[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2a2da905[object: org.codehaus.groovy.ast.expr.MethodCallExpression@24f360b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60cf80e7[ConstantExpression[*.{txt,pdf,r,xls}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@302fec27[org.codehaus.groovy.ast.expr.VariableExpression@770d0ea6[variable: rseqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@48c40605[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@54107f42[org.codehaus.groovy.ast.expr.VariableExpression@1b11ef33[variable: strandRule]("=" at 538:5:  "=" )org.codehaus.groovy.ast.expr.ElvisOperatorExpression@476aac9[org.codehaus.groovy.ast.expr.BooleanExpression@6cea706c ? org.codehaus.groovy.ast.expr.PropertyExpression@3bd7f8dc[object: org.codehaus.groovy.ast.expr.VariableExpression@2f2bf0e2[variable: params] property: ConstantExpression[strandRule]] : org.codehaus.groovy.ast.expr.TernaryExpression@1eba372c[org.codehaus.groovy.ast.expr.BooleanExpression@21ec5d87 ? ConstantExpression[++,--] : ConstantExpression[1+-,1-+,2++,2--]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25f9407e[expression:org.codehaus.groovy.ast.expr.GStringExpression@552518c3[strings: [ConstantExpression[
    samtools index ], ConstantExpression[
    infer_experiment.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.infer_experiment.txt
    RPKM_saturation.py -i ], ConstantExpression[ -r ], ConstantExpression[ -d ], ConstantExpression[ -o ], ConstantExpression[.RPKM_saturation
    junction_annotation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    bam_stat.py -i ], ConstantExpression[ 2> ], ConstantExpression[.bam_stat.txt
    junction_saturation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[ 2> ], ConstantExpression[.junction_annotation_log.txt
    inner_distance.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    geneBody_coverage.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    read_distribution.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.read_distribution.txt
    read_duplication.py -i ], ConstantExpression[ -o ], ConstantExpression[.read_duplication
    echo "Filename ], ConstantExpression[ RseQC version: "$(read_duplication.py --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1a69561c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@59aa20b3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@363f6148[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@4b21844c[object: org.codehaus.groovy.ast.expr.VariableExpression@1b28f282[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@138fe6ec[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@5e77f0f4[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@19b30c92[variable: strandRule], org.codehaus.groovy.ast.expr.PropertyExpression@455351c4[object: org.codehaus.groovy.ast.expr.VariableExpression@29876704[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4816c290[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@4940809c[object: org.codehaus.groovy.ast.expr.VariableExpression@16423501[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4efcf8a[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@7a138fc5[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@379ab47b[object: org.codehaus.groovy.ast.expr.VariableExpression@307765b4[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4a9e6faf[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2c95ac9e[object: org.codehaus.groovy.ast.expr.VariableExpression@4e4efc1b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@459f7aa3[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@7cc586a8[object: org.codehaus.groovy.ast.expr.VariableExpression@7db534f2[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@44a2b17b[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@7a56812e[object: org.codehaus.groovy.ast.expr.VariableExpression@2a76b80a[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@7eb01b12[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@2f4854d6[object: org.codehaus.groovy.ast.expr.VariableExpression@61d9efe0[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@7e70bd39[object: org.codehaus.groovy.ast.expr.VariableExpression@e6516e[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6de54b40[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@43ed0ff3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@388ffbc2[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@a50b09c[object: org.codehaus.groovy.ast.expr.VariableExpression@4da855dd[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6691490c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2187fff7[object: org.codehaus.groovy.ast.expr.VariableExpression@2e5c7f0b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@21d5c1a0[variable: bam_rseqc]]]]] }]]]
Nov-14 16:09:26.624 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: rseqc with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@4c36250e[org.codehaus.groovy.ast.expr.ClosureExpression@21526f6c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@49f5c307[org.codehaus.groovy.ast.stmt.ExpressionStatement@299266e2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5471388b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@66ea1466[org.codehaus.groovy.ast.expr.GStringExpression@1601e47[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@3bffddff[variable: bam_rseqc]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66971f6b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50687efb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@517bd097[org.codehaus.groovy.ast.expr.MapExpression@142eef62[org.codehaus.groovy.ast.expr.MapEntryExpression@4a9cc6cb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@5990e6c5[strings: [ConstantExpression[], ConstantExpression[/rseqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@56e07a08[object: org.codehaus.groovy.ast.expr.VariableExpression@35d6ca49[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1950e8a6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@47289387[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12cd9150[org.codehaus.groovy.ast.expr.ClosureExpression@114a85c2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@f415a95[org.codehaus.groovy.ast.stmt.ExpressionStatement@cf65451[expression:org.codehaus.groovy.ast.expr.BinaryExpression@724f138e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37eeec90[org.codehaus.groovy.ast.expr.BooleanExpression@32fe9d0a ? org.codehaus.groovy.ast.expr.PropertyExpression@c9413d8[object: org.codehaus.groovy.ast.expr.VariableExpression@64da2a7[variable: params] property: ConstantExpression[rseqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@46074492[object: ConstantExpression[32] property: ConstantExpression[GB]]]("*" at 512:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@d78795[object: org.codehaus.groovy.ast.expr.VariableExpression@2c715e84[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47428937[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b9d6699[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7caa550[org.codehaus.groovy.ast.expr.ClosureExpression@21694e53[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72b16078[org.codehaus.groovy.ast.stmt.ExpressionStatement@22c86919[expression:org.codehaus.groovy.ast.expr.BinaryExpression@70fab835[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1b0a7baf[org.codehaus.groovy.ast.expr.BooleanExpression@62417a16 ? org.codehaus.groovy.ast.expr.PropertyExpression@32057e6[object: org.codehaus.groovy.ast.expr.VariableExpression@26be6ca7[variable: params] property: ConstantExpression[rseqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6ea1bcdc[object: ConstantExpression[7] property: ConstantExpression[h]]]("*" at 513:39:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@759fad4[object: org.codehaus.groovy.ast.expr.VariableExpression@64712be[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@53499d85[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@30ed9c6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@782a4fff[org.codehaus.groovy.ast.expr.VariableExpression@46c670a6[variable: bam_rseqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@59fc684e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ae81e1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fd1731c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5ae76500[org.codehaus.groovy.ast.expr.VariableExpression@6063d80a[variable: bed12]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1133ec6e[org.codehaus.groovy.ast.expr.VariableExpression@355e34c7[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54709809[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2a2da905[object: org.codehaus.groovy.ast.expr.MethodCallExpression@24f360b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60cf80e7[ConstantExpression[*.{txt,pdf,r,xls}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@302fec27[org.codehaus.groovy.ast.expr.VariableExpression@770d0ea6[variable: rseqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@48c40605[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@54107f42[org.codehaus.groovy.ast.expr.VariableExpression@1b11ef33[variable: strandRule]("=" at 538:5:  "=" )org.codehaus.groovy.ast.expr.ElvisOperatorExpression@476aac9[org.codehaus.groovy.ast.expr.BooleanExpression@6cea706c ? org.codehaus.groovy.ast.expr.PropertyExpression@3bd7f8dc[object: org.codehaus.groovy.ast.expr.VariableExpression@2f2bf0e2[variable: params] property: ConstantExpression[strandRule]] : org.codehaus.groovy.ast.expr.TernaryExpression@1eba372c[org.codehaus.groovy.ast.expr.BooleanExpression@21ec5d87 ? ConstantExpression[++,--] : ConstantExpression[1+-,1-+,2++,2--]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25f9407e[expression:org.codehaus.groovy.ast.expr.GStringExpression@552518c3[strings: [ConstantExpression[
    samtools index ], ConstantExpression[
    infer_experiment.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.infer_experiment.txt
    RPKM_saturation.py -i ], ConstantExpression[ -r ], ConstantExpression[ -d ], ConstantExpression[ -o ], ConstantExpression[.RPKM_saturation
    junction_annotation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    bam_stat.py -i ], ConstantExpression[ 2> ], ConstantExpression[.bam_stat.txt
    junction_saturation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[ 2> ], ConstantExpression[.junction_annotation_log.txt
    inner_distance.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    geneBody_coverage.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    read_distribution.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.read_distribution.txt
    read_duplication.py -i ], ConstantExpression[ -o ], ConstantExpression[.read_duplication
    echo "Filename ], ConstantExpression[ RseQC version: "$(read_duplication.py --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1a69561c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@59aa20b3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@363f6148[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@4b21844c[object: org.codehaus.groovy.ast.expr.VariableExpression@1b28f282[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@138fe6ec[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@5e77f0f4[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@19b30c92[variable: strandRule], org.codehaus.groovy.ast.expr.PropertyExpression@455351c4[object: org.codehaus.groovy.ast.expr.VariableExpression@29876704[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4816c290[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@4940809c[object: org.codehaus.groovy.ast.expr.VariableExpression@16423501[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4efcf8a[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@7a138fc5[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@379ab47b[object: org.codehaus.groovy.ast.expr.VariableExpression@307765b4[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4a9e6faf[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2c95ac9e[object: org.codehaus.groovy.ast.expr.VariableExpression@4e4efc1b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@459f7aa3[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@7cc586a8[object: org.codehaus.groovy.ast.expr.VariableExpression@7db534f2[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@44a2b17b[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@7a56812e[object: org.codehaus.groovy.ast.expr.VariableExpression@2a76b80a[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@7eb01b12[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@2f4854d6[object: org.codehaus.groovy.ast.expr.VariableExpression@61d9efe0[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@7e70bd39[object: org.codehaus.groovy.ast.expr.VariableExpression@e6516e[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6de54b40[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@43ed0ff3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@388ffbc2[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@a50b09c[object: org.codehaus.groovy.ast.expr.VariableExpression@4da855dd[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6691490c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2187fff7[object: org.codehaus.groovy.ast.expr.VariableExpression@2e5c7f0b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@21d5c1a0[variable: bam_rseqc]]]]] }]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@4de025bf[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4c36250e[ConstantExpression[rseqc], org.codehaus.groovy.ast.expr.ClosureExpression@21526f6c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@49f5c307[org.codehaus.groovy.ast.stmt.ExpressionStatement@299266e2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5471388b[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@66ea1466[org.codehaus.groovy.ast.expr.GStringExpression@1601e47[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@3bffddff[variable: bam_rseqc]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66971f6b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50687efb[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@517bd097[org.codehaus.groovy.ast.expr.MapExpression@142eef62[org.codehaus.groovy.ast.expr.MapEntryExpression@4a9cc6cb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@5990e6c5[strings: [ConstantExpression[], ConstantExpression[/rseqc]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@56e07a08[object: org.codehaus.groovy.ast.expr.VariableExpression@35d6ca49[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1950e8a6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@47289387[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@12cd9150[org.codehaus.groovy.ast.expr.ClosureExpression@114a85c2[]{ org.codehaus.groovy.ast.stmt.BlockStatement@f415a95[org.codehaus.groovy.ast.stmt.ExpressionStatement@cf65451[expression:org.codehaus.groovy.ast.expr.BinaryExpression@724f138e[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37eeec90[org.codehaus.groovy.ast.expr.BooleanExpression@32fe9d0a ? org.codehaus.groovy.ast.expr.PropertyExpression@c9413d8[object: org.codehaus.groovy.ast.expr.VariableExpression@64da2a7[variable: params] property: ConstantExpression[rseqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@46074492[object: ConstantExpression[32] property: ConstantExpression[GB]]]("*" at 512:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@d78795[object: org.codehaus.groovy.ast.expr.VariableExpression@2c715e84[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@47428937[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b9d6699[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7caa550[org.codehaus.groovy.ast.expr.ClosureExpression@21694e53[]{ org.codehaus.groovy.ast.stmt.BlockStatement@72b16078[org.codehaus.groovy.ast.stmt.ExpressionStatement@22c86919[expression:org.codehaus.groovy.ast.expr.BinaryExpression@70fab835[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1b0a7baf[org.codehaus.groovy.ast.expr.BooleanExpression@62417a16 ? org.codehaus.groovy.ast.expr.PropertyExpression@32057e6[object: org.codehaus.groovy.ast.expr.VariableExpression@26be6ca7[variable: params] property: ConstantExpression[rseqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6ea1bcdc[object: ConstantExpression[7] property: ConstantExpression[h]]]("*" at 513:39:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@759fad4[object: org.codehaus.groovy.ast.expr.VariableExpression@64712be[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@53499d85[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@30ed9c6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@782a4fff[org.codehaus.groovy.ast.expr.VariableExpression@46c670a6[variable: bam_rseqc]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@59fc684e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5ae81e1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fd1731c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5ae76500[org.codehaus.groovy.ast.expr.VariableExpression@6063d80a[variable: bed12]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1133ec6e[org.codehaus.groovy.ast.expr.VariableExpression@355e34c7[variable: bed12]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54709809[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2a2da905[object: org.codehaus.groovy.ast.expr.MethodCallExpression@24f360b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60cf80e7[ConstantExpression[*.{txt,pdf,r,xls}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@302fec27[org.codehaus.groovy.ast.expr.VariableExpression@770d0ea6[variable: rseqc_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@48c40605[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@54107f42[org.codehaus.groovy.ast.expr.VariableExpression@1b11ef33[variable: strandRule]("=" at 538:5:  "=" )org.codehaus.groovy.ast.expr.ElvisOperatorExpression@476aac9[org.codehaus.groovy.ast.expr.BooleanExpression@6cea706c ? org.codehaus.groovy.ast.expr.PropertyExpression@3bd7f8dc[object: org.codehaus.groovy.ast.expr.VariableExpression@2f2bf0e2[variable: params] property: ConstantExpression[strandRule]] : org.codehaus.groovy.ast.expr.TernaryExpression@1eba372c[org.codehaus.groovy.ast.expr.BooleanExpression@21ec5d87 ? ConstantExpression[++,--] : ConstantExpression[1+-,1-+,2++,2--]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25f9407e[expression:org.codehaus.groovy.ast.expr.GStringExpression@552518c3[strings: [ConstantExpression[
    samtools index ], ConstantExpression[
    infer_experiment.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.infer_experiment.txt
    RPKM_saturation.py -i ], ConstantExpression[ -r ], ConstantExpression[ -d ], ConstantExpression[ -o ], ConstantExpression[.RPKM_saturation
    junction_annotation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    bam_stat.py -i ], ConstantExpression[ 2> ], ConstantExpression[.bam_stat.txt
    junction_saturation.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[ 2> ], ConstantExpression[.junction_annotation_log.txt
    inner_distance.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    geneBody_coverage.py -i ], ConstantExpression[ -o ], ConstantExpression[.rseqc -r ], ConstantExpression[
    read_distribution.py -i ], ConstantExpression[ -r ], ConstantExpression[ > ], ConstantExpression[.read_distribution.txt
    read_duplication.py -i ], ConstantExpression[ -o ], ConstantExpression[.read_duplication
    echo "Filename ], ConstantExpression[ RseQC version: "$(read_duplication.py --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@1a69561c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@59aa20b3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@363f6148[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@4b21844c[object: org.codehaus.groovy.ast.expr.VariableExpression@1b28f282[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@138fe6ec[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@5e77f0f4[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@19b30c92[variable: strandRule], org.codehaus.groovy.ast.expr.PropertyExpression@455351c4[object: org.codehaus.groovy.ast.expr.VariableExpression@29876704[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4816c290[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@4940809c[object: org.codehaus.groovy.ast.expr.VariableExpression@16423501[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4efcf8a[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@7a138fc5[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@379ab47b[object: org.codehaus.groovy.ast.expr.VariableExpression@307765b4[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@4a9e6faf[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2c95ac9e[object: org.codehaus.groovy.ast.expr.VariableExpression@4e4efc1b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@459f7aa3[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@7cc586a8[object: org.codehaus.groovy.ast.expr.VariableExpression@7db534f2[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@44a2b17b[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@7a56812e[object: org.codehaus.groovy.ast.expr.VariableExpression@2a76b80a[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@7eb01b12[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@2f4854d6[object: org.codehaus.groovy.ast.expr.VariableExpression@61d9efe0[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@7e70bd39[object: org.codehaus.groovy.ast.expr.VariableExpression@e6516e[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6de54b40[variable: bed12], org.codehaus.groovy.ast.expr.VariableExpression@43ed0ff3[variable: bam_rseqc], org.codehaus.groovy.ast.expr.VariableExpression@388ffbc2[variable: bed12], org.codehaus.groovy.ast.expr.PropertyExpression@a50b09c[object: org.codehaus.groovy.ast.expr.VariableExpression@4da855dd[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6691490c[variable: bam_rseqc], org.codehaus.groovy.ast.expr.PropertyExpression@2187fff7[object: org.codehaus.groovy.ast.expr.VariableExpression@2e5c7f0b[variable: bam_rseqc] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@21d5c1a0[variable: bam_rseqc]]]]] }]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@30ed9c6c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@782a4fff[org.codehaus.groovy.ast.expr.VariableExpression@46c670a6[variable: bam_rseqc]]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5ae81e1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2fd1731c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5ae76500[org.codehaus.groovy.ast.expr.VariableExpression@6063d80a[variable: bed12]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1133ec6e[org.codehaus.groovy.ast.expr.VariableExpression@355e34c7[variable: bed12]]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2fd1731c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5ae76500[org.codehaus.groovy.ast.expr.VariableExpression@6063d80a[variable: bed12]]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2a2da905[object: org.codehaus.groovy.ast.expr.MethodCallExpression@24f360b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60cf80e7[ConstantExpression[*.{txt,pdf,r,xls}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@302fec27[org.codehaus.groovy.ast.expr.VariableExpression@770d0ea6[variable: rseqc_results]]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@24f360b2[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@60cf80e7[ConstantExpression[*.{txt,pdf,r,xls}]]]
Nov-14 16:09:26.625 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.628 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@538613b3[org.codehaus.groovy.ast.expr.MethodCallExpression@1eef9aef[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[preseq] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11389053[org.codehaus.groovy.ast.expr.ClosureExpression@5db99216[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ec11999[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c1bd44c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9f46d94[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18cc679e[org.codehaus.groovy.ast.expr.GStringExpression@2e77b8cf[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2c4ca0f9[variable: bam_preseq]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67ef029[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7df587ef[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e57e95e[org.codehaus.groovy.ast.expr.MapExpression@2755d705[org.codehaus.groovy.ast.expr.MapEntryExpression@56db847e(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@740abb5[strings: [ConstantExpression[], ConstantExpression[/preseq]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@560cbf1a[object: org.codehaus.groovy.ast.expr.VariableExpression@5fe8b721[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@551a20d6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@578524c3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64c2b546[org.codehaus.groovy.ast.expr.ClosureExpression@7e094740[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a11c4c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@4cc547a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@7555b920[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4152d38d[org.codehaus.groovy.ast.expr.BooleanExpression@3591009c ? org.codehaus.groovy.ast.expr.PropertyExpression@5398edd0[object: org.codehaus.groovy.ast.expr.VariableExpression@b5cc23a[variable: params] property: ConstantExpression[preseq_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@5cc5b667[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 564:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@61edc883[object: org.codehaus.groovy.ast.expr.VariableExpression@758f4f03[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@182f1e9a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6928f576[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@660e9100[org.codehaus.groovy.ast.expr.ClosureExpression@69f63d95[]{ org.codehaus.groovy.ast.stmt.BlockStatement@9cd25ff[org.codehaus.groovy.ast.stmt.ExpressionStatement@27e0f2f5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3574e198[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6db66836[org.codehaus.groovy.ast.expr.BooleanExpression@db44aa2 ? org.codehaus.groovy.ast.expr.PropertyExpression@2de366bb[object: org.codehaus.groovy.ast.expr.VariableExpression@3f093abe[variable: params] property: ConstantExpression[preseq_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@61a002b1[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 565:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4eeea57d[object: org.codehaus.groovy.ast.expr.VariableExpression@780ec4a5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@e24ddd0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f70f32f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@548e76f1[org.codehaus.groovy.ast.expr.VariableExpression@5aabbb29[variable: bam_preseq]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@72c927f1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ac85b0c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3dd69f5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aa3193a[org.codehaus.groovy.ast.expr.GStringExpression@1ee4730[strings: [ConstantExpression[], ConstantExpression[.ccurve.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@59a67c3a[object: org.codehaus.groovy.ast.expr.VariableExpression@5003041b[variable: bam_preseq] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@724bade8[org.codehaus.groovy.ast.expr.VariableExpression@16fb356[variable: preseq_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6bc248ed[expression:org.codehaus.groovy.ast.expr.GStringExpression@23a9ba52[strings: [ConstantExpression[
    preseq lc_extrap -v -B ], ConstantExpression[ -o ], ConstantExpression[.ccurve.txt
    echo "File name: ], ConstantExpression[  preseq version: "$(preseq)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@ca27722[variable: bam_preseq], org.codehaus.groovy.ast.expr.PropertyExpression@70ab80e3[object: org.codehaus.groovy.ast.expr.VariableExpression@9573b3b[variable: bam_preseq] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@67427b69[variable: bam_preseq]]]]] }]]]
Nov-14 16:09:26.628 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: preseq with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@11389053[org.codehaus.groovy.ast.expr.ClosureExpression@5db99216[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ec11999[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c1bd44c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9f46d94[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18cc679e[org.codehaus.groovy.ast.expr.GStringExpression@2e77b8cf[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2c4ca0f9[variable: bam_preseq]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67ef029[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7df587ef[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e57e95e[org.codehaus.groovy.ast.expr.MapExpression@2755d705[org.codehaus.groovy.ast.expr.MapEntryExpression@56db847e(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@740abb5[strings: [ConstantExpression[], ConstantExpression[/preseq]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@560cbf1a[object: org.codehaus.groovy.ast.expr.VariableExpression@5fe8b721[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@551a20d6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@578524c3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64c2b546[org.codehaus.groovy.ast.expr.ClosureExpression@7e094740[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a11c4c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@4cc547a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@7555b920[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4152d38d[org.codehaus.groovy.ast.expr.BooleanExpression@3591009c ? org.codehaus.groovy.ast.expr.PropertyExpression@5398edd0[object: org.codehaus.groovy.ast.expr.VariableExpression@b5cc23a[variable: params] property: ConstantExpression[preseq_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@5cc5b667[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 564:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@61edc883[object: org.codehaus.groovy.ast.expr.VariableExpression@758f4f03[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@182f1e9a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6928f576[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@660e9100[org.codehaus.groovy.ast.expr.ClosureExpression@69f63d95[]{ org.codehaus.groovy.ast.stmt.BlockStatement@9cd25ff[org.codehaus.groovy.ast.stmt.ExpressionStatement@27e0f2f5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3574e198[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6db66836[org.codehaus.groovy.ast.expr.BooleanExpression@db44aa2 ? org.codehaus.groovy.ast.expr.PropertyExpression@2de366bb[object: org.codehaus.groovy.ast.expr.VariableExpression@3f093abe[variable: params] property: ConstantExpression[preseq_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@61a002b1[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 565:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4eeea57d[object: org.codehaus.groovy.ast.expr.VariableExpression@780ec4a5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@e24ddd0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f70f32f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@548e76f1[org.codehaus.groovy.ast.expr.VariableExpression@5aabbb29[variable: bam_preseq]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@72c927f1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ac85b0c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3dd69f5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aa3193a[org.codehaus.groovy.ast.expr.GStringExpression@1ee4730[strings: [ConstantExpression[], ConstantExpression[.ccurve.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@59a67c3a[object: org.codehaus.groovy.ast.expr.VariableExpression@5003041b[variable: bam_preseq] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@724bade8[org.codehaus.groovy.ast.expr.VariableExpression@16fb356[variable: preseq_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6bc248ed[expression:org.codehaus.groovy.ast.expr.GStringExpression@23a9ba52[strings: [ConstantExpression[
    preseq lc_extrap -v -B ], ConstantExpression[ -o ], ConstantExpression[.ccurve.txt
    echo "File name: ], ConstantExpression[  preseq version: "$(preseq)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@ca27722[variable: bam_preseq], org.codehaus.groovy.ast.expr.PropertyExpression@70ab80e3[object: org.codehaus.groovy.ast.expr.VariableExpression@9573b3b[variable: bam_preseq] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@67427b69[variable: bam_preseq]]]]] }]
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@78461bc4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@11389053[ConstantExpression[preseq], org.codehaus.groovy.ast.expr.ClosureExpression@5db99216[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ec11999[org.codehaus.groovy.ast.stmt.ExpressionStatement@5c1bd44c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@9f46d94[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@18cc679e[org.codehaus.groovy.ast.expr.GStringExpression@2e77b8cf[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2c4ca0f9[variable: bam_preseq]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@67ef029[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7df587ef[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e57e95e[org.codehaus.groovy.ast.expr.MapExpression@2755d705[org.codehaus.groovy.ast.expr.MapEntryExpression@56db847e(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@740abb5[strings: [ConstantExpression[], ConstantExpression[/preseq]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@560cbf1a[object: org.codehaus.groovy.ast.expr.VariableExpression@5fe8b721[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@551a20d6[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@578524c3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@64c2b546[org.codehaus.groovy.ast.expr.ClosureExpression@7e094740[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7a11c4c7[org.codehaus.groovy.ast.stmt.ExpressionStatement@4cc547a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@7555b920[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@4152d38d[org.codehaus.groovy.ast.expr.BooleanExpression@3591009c ? org.codehaus.groovy.ast.expr.PropertyExpression@5398edd0[object: org.codehaus.groovy.ast.expr.VariableExpression@b5cc23a[variable: params] property: ConstantExpression[preseq_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@5cc5b667[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 564:45:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@61edc883[object: org.codehaus.groovy.ast.expr.VariableExpression@758f4f03[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@182f1e9a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6928f576[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@660e9100[org.codehaus.groovy.ast.expr.ClosureExpression@69f63d95[]{ org.codehaus.groovy.ast.stmt.BlockStatement@9cd25ff[org.codehaus.groovy.ast.stmt.ExpressionStatement@27e0f2f5[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3574e198[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6db66836[org.codehaus.groovy.ast.expr.BooleanExpression@db44aa2 ? org.codehaus.groovy.ast.expr.PropertyExpression@2de366bb[object: org.codehaus.groovy.ast.expr.VariableExpression@3f093abe[variable: params] property: ConstantExpression[preseq_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@61a002b1[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 565:40:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4eeea57d[object: org.codehaus.groovy.ast.expr.VariableExpression@780ec4a5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@e24ddd0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f70f32f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@548e76f1[org.codehaus.groovy.ast.expr.VariableExpression@5aabbb29[variable: bam_preseq]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@72c927f1[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1ac85b0c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3dd69f5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aa3193a[org.codehaus.groovy.ast.expr.GStringExpression@1ee4730[strings: [ConstantExpression[], ConstantExpression[.ccurve.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@59a67c3a[object: org.codehaus.groovy.ast.expr.VariableExpression@5003041b[variable: bam_preseq] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@724bade8[org.codehaus.groovy.ast.expr.VariableExpression@16fb356[variable: preseq_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6bc248ed[expression:org.codehaus.groovy.ast.expr.GStringExpression@23a9ba52[strings: [ConstantExpression[
    preseq lc_extrap -v -B ], ConstantExpression[ -o ], ConstantExpression[.ccurve.txt
    echo "File name: ], ConstantExpression[  preseq version: "$(preseq)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@ca27722[variable: bam_preseq], org.codehaus.groovy.ast.expr.PropertyExpression@70ab80e3[object: org.codehaus.groovy.ast.expr.VariableExpression@9573b3b[variable: bam_preseq] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@67427b69[variable: bam_preseq]]]]] }]]
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6f70f32f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@548e76f1[org.codehaus.groovy.ast.expr.VariableExpression@5aabbb29[variable: bam_preseq]]]
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1ac85b0c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3dd69f5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aa3193a[org.codehaus.groovy.ast.expr.GStringExpression@1ee4730[strings: [ConstantExpression[], ConstantExpression[.ccurve.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@544630b7null{ org.codehaus.groovy.ast.stmt.BlockStatement@64f857e7[org.codehaus.groovy.ast.stmt.ExpressionStatement@1095f122[expression:org.codehaus.groovy.ast.expr.PropertyExpression@59a67c3a[object: org.codehaus.groovy.ast.expr.VariableExpression@5003041b[variable: bam_preseq] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@724bade8[org.codehaus.groovy.ast.expr.VariableExpression@16fb356[variable: preseq_results]]]
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3dd69f5a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aa3193a[org.codehaus.groovy.ast.expr.GStringExpression@1ee4730[strings: [ConstantExpression[], ConstantExpression[.ccurve.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@544630b7null{ org.codehaus.groovy.ast.stmt.BlockStatement@64f857e7[org.codehaus.groovy.ast.stmt.ExpressionStatement@1095f122[expression:org.codehaus.groovy.ast.expr.PropertyExpression@59a67c3a[object: org.codehaus.groovy.ast.expr.VariableExpression@5003041b[variable: bam_preseq] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.629 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.630 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@58c540cf[org.codehaus.groovy.ast.expr.MethodCallExpression@3d6300e8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[markDuplicates] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b822fcc[org.codehaus.groovy.ast.expr.ClosureExpression@24a1c17f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@56102e1c[org.codehaus.groovy.ast.stmt.ExpressionStatement@73511076[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7927bd9f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@532721fd[org.codehaus.groovy.ast.expr.GStringExpression@410954b[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7fb9f71f[variable: bam_markduplicates]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3b366632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@51f49060[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@514eedd8[org.codehaus.groovy.ast.expr.MapExpression@617fe9e1[org.codehaus.groovy.ast.expr.MapEntryExpression@6970140a(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@1cf2fed4[strings: [ConstantExpression[], ConstantExpression[/markDuplicates]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3af4e0bf[object: org.codehaus.groovy.ast.expr.VariableExpression@245a26e1[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4d63b624[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@466cf502[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5b800468[org.codehaus.groovy.ast.expr.ClosureExpression@2e185cd7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7e1a1da6[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f7f2382[expression:org.codehaus.groovy.ast.expr.BinaryExpression@407cf41[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6815c5f2[org.codehaus.groovy.ast.expr.BooleanExpression@46cc127b ? org.codehaus.groovy.ast.expr.PropertyExpression@60094a13[object: org.codehaus.groovy.ast.expr.VariableExpression@5aceec94[variable: params] property: ConstantExpression[markDuplicates_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c32886a[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 588:54:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@3a4b0e5d[object: org.codehaus.groovy.ast.expr.VariableExpression@10b892d5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d3f761a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3546d80f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@579d011c[org.codehaus.groovy.ast.expr.ClosureExpression@3670f00[]{ org.codehaus.groovy.ast.stmt.BlockStatement@452e26d0[org.codehaus.groovy.ast.stmt.ExpressionStatement@46ab18da[expression:org.codehaus.groovy.ast.expr.BinaryExpression@790174f2[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@42257bdd[org.codehaus.groovy.ast.expr.BooleanExpression@7689ddef ? org.codehaus.groovy.ast.expr.PropertyExpression@687a762c[object: org.codehaus.groovy.ast.expr.VariableExpression@1a2e2935[variable: params] property: ConstantExpression[markDuplicates_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@733c423e[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 589:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4b629f13[object: org.codehaus.groovy.ast.expr.VariableExpression@70925b45[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1b9ea3e3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@aa22f1c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@55e7a35c[org.codehaus.groovy.ast.expr.VariableExpression@37cd92d6[variable: bam_markduplicates]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5922ae77[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4263b080[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2af616d3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71f67a79[org.codehaus.groovy.ast.expr.GStringExpression@3deb2326[strings: [ConstantExpression[], ConstantExpression[.markDups.bam]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62d363ab[object: org.codehaus.groovy.ast.expr.VariableExpression@7889a1ac[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aee3976[org.codehaus.groovy.ast.expr.VariableExpression@5ef8df1e[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@27cf3151[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@127e70c5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5910de75[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4108fa66[org.codehaus.groovy.ast.expr.GStringExpression@1f130eaf[strings: [ConstantExpression[], ConstantExpression[.markDups_metrics.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7e0aadd0[object: org.codehaus.groovy.ast.expr.VariableExpression@21362712[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27eb3298[org.codehaus.groovy.ast.expr.VariableExpression@200a26bc[variable: picard_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@bc57b40[expression:org.codehaus.groovy.ast.expr.GStringExpression@1b5bc39d[strings: [ConstantExpression[
    java -Xmx2g -jar $PICARD_HOME/picard.jar MarkDuplicates \
        INPUT=], ConstantExpression[ \
        OUTPUT=], ConstantExpression[.markDups.bam \
        METRICS_FILE=], ConstantExpression[.markDups_metrics.txt \
        REMOVE_DUPLICATES=false \
        ASSUME_SORTED=true \
        PROGRAM_RECORD_ID='null' \
        VALIDATION_STRINGENCY=LENIENT

    # Print version number to standard out
    echo "File name: ], ConstantExpression[ Picard version "$(java -Xmx2g -jar $PICARD_HOME/picard.jar  MarkDuplicates --version 2>&1)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@655a5d9c[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.PropertyExpression@1494b84d[object: org.codehaus.groovy.ast.expr.VariableExpression@34abdee4[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@71a9b4c7[object: org.codehaus.groovy.ast.expr.VariableExpression@4628b1d3[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@77cf3f8b[variable: bam_markduplicates]]]]] }]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: markDuplicates with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b822fcc[org.codehaus.groovy.ast.expr.ClosureExpression@24a1c17f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@56102e1c[org.codehaus.groovy.ast.stmt.ExpressionStatement@73511076[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7927bd9f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@532721fd[org.codehaus.groovy.ast.expr.GStringExpression@410954b[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7fb9f71f[variable: bam_markduplicates]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3b366632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@51f49060[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@514eedd8[org.codehaus.groovy.ast.expr.MapExpression@617fe9e1[org.codehaus.groovy.ast.expr.MapEntryExpression@6970140a(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@1cf2fed4[strings: [ConstantExpression[], ConstantExpression[/markDuplicates]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3af4e0bf[object: org.codehaus.groovy.ast.expr.VariableExpression@245a26e1[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4d63b624[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@466cf502[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5b800468[org.codehaus.groovy.ast.expr.ClosureExpression@2e185cd7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7e1a1da6[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f7f2382[expression:org.codehaus.groovy.ast.expr.BinaryExpression@407cf41[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6815c5f2[org.codehaus.groovy.ast.expr.BooleanExpression@46cc127b ? org.codehaus.groovy.ast.expr.PropertyExpression@60094a13[object: org.codehaus.groovy.ast.expr.VariableExpression@5aceec94[variable: params] property: ConstantExpression[markDuplicates_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c32886a[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 588:54:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@3a4b0e5d[object: org.codehaus.groovy.ast.expr.VariableExpression@10b892d5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d3f761a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3546d80f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@579d011c[org.codehaus.groovy.ast.expr.ClosureExpression@3670f00[]{ org.codehaus.groovy.ast.stmt.BlockStatement@452e26d0[org.codehaus.groovy.ast.stmt.ExpressionStatement@46ab18da[expression:org.codehaus.groovy.ast.expr.BinaryExpression@790174f2[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@42257bdd[org.codehaus.groovy.ast.expr.BooleanExpression@7689ddef ? org.codehaus.groovy.ast.expr.PropertyExpression@687a762c[object: org.codehaus.groovy.ast.expr.VariableExpression@1a2e2935[variable: params] property: ConstantExpression[markDuplicates_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@733c423e[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 589:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4b629f13[object: org.codehaus.groovy.ast.expr.VariableExpression@70925b45[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1b9ea3e3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@aa22f1c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@55e7a35c[org.codehaus.groovy.ast.expr.VariableExpression@37cd92d6[variable: bam_markduplicates]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5922ae77[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4263b080[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2af616d3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71f67a79[org.codehaus.groovy.ast.expr.GStringExpression@3deb2326[strings: [ConstantExpression[], ConstantExpression[.markDups.bam]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62d363ab[object: org.codehaus.groovy.ast.expr.VariableExpression@7889a1ac[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aee3976[org.codehaus.groovy.ast.expr.VariableExpression@5ef8df1e[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@27cf3151[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@127e70c5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5910de75[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4108fa66[org.codehaus.groovy.ast.expr.GStringExpression@1f130eaf[strings: [ConstantExpression[], ConstantExpression[.markDups_metrics.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7e0aadd0[object: org.codehaus.groovy.ast.expr.VariableExpression@21362712[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27eb3298[org.codehaus.groovy.ast.expr.VariableExpression@200a26bc[variable: picard_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@bc57b40[expression:org.codehaus.groovy.ast.expr.GStringExpression@1b5bc39d[strings: [ConstantExpression[
    java -Xmx2g -jar $PICARD_HOME/picard.jar MarkDuplicates \
        INPUT=], ConstantExpression[ \
        OUTPUT=], ConstantExpression[.markDups.bam \
        METRICS_FILE=], ConstantExpression[.markDups_metrics.txt \
        REMOVE_DUPLICATES=false \
        ASSUME_SORTED=true \
        PROGRAM_RECORD_ID='null' \
        VALIDATION_STRINGENCY=LENIENT

    # Print version number to standard out
    echo "File name: ], ConstantExpression[ Picard version "$(java -Xmx2g -jar $PICARD_HOME/picard.jar  MarkDuplicates --version 2>&1)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@655a5d9c[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.PropertyExpression@1494b84d[object: org.codehaus.groovy.ast.expr.VariableExpression@34abdee4[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@71a9b4c7[object: org.codehaus.groovy.ast.expr.VariableExpression@4628b1d3[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@77cf3f8b[variable: bam_markduplicates]]]]] }]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@1df98368[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b822fcc[ConstantExpression[markDuplicates], org.codehaus.groovy.ast.expr.ClosureExpression@24a1c17f[]{ org.codehaus.groovy.ast.stmt.BlockStatement@56102e1c[org.codehaus.groovy.ast.stmt.ExpressionStatement@73511076[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@7927bd9f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@532721fd[org.codehaus.groovy.ast.expr.GStringExpression@410954b[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7fb9f71f[variable: bam_markduplicates]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3b366632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@51f49060[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@514eedd8[org.codehaus.groovy.ast.expr.MapExpression@617fe9e1[org.codehaus.groovy.ast.expr.MapEntryExpression@6970140a(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@1cf2fed4[strings: [ConstantExpression[], ConstantExpression[/markDuplicates]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3af4e0bf[object: org.codehaus.groovy.ast.expr.VariableExpression@245a26e1[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4d63b624[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@466cf502[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5b800468[org.codehaus.groovy.ast.expr.ClosureExpression@2e185cd7[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7e1a1da6[org.codehaus.groovy.ast.stmt.ExpressionStatement@5f7f2382[expression:org.codehaus.groovy.ast.expr.BinaryExpression@407cf41[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@6815c5f2[org.codehaus.groovy.ast.expr.BooleanExpression@46cc127b ? org.codehaus.groovy.ast.expr.PropertyExpression@60094a13[object: org.codehaus.groovy.ast.expr.VariableExpression@5aceec94[variable: params] property: ConstantExpression[markDuplicates_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1c32886a[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 588:54:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@3a4b0e5d[object: org.codehaus.groovy.ast.expr.VariableExpression@10b892d5[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d3f761a[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3546d80f[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@579d011c[org.codehaus.groovy.ast.expr.ClosureExpression@3670f00[]{ org.codehaus.groovy.ast.stmt.BlockStatement@452e26d0[org.codehaus.groovy.ast.stmt.ExpressionStatement@46ab18da[expression:org.codehaus.groovy.ast.expr.BinaryExpression@790174f2[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@42257bdd[org.codehaus.groovy.ast.expr.BooleanExpression@7689ddef ? org.codehaus.groovy.ast.expr.PropertyExpression@687a762c[object: org.codehaus.groovy.ast.expr.VariableExpression@1a2e2935[variable: params] property: ConstantExpression[markDuplicates_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@733c423e[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 589:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@4b629f13[object: org.codehaus.groovy.ast.expr.VariableExpression@70925b45[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1b9ea3e3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@aa22f1c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@55e7a35c[org.codehaus.groovy.ast.expr.VariableExpression@37cd92d6[variable: bam_markduplicates]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5922ae77[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4263b080[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2af616d3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71f67a79[org.codehaus.groovy.ast.expr.GStringExpression@3deb2326[strings: [ConstantExpression[], ConstantExpression[.markDups.bam]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62d363ab[object: org.codehaus.groovy.ast.expr.VariableExpression@7889a1ac[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aee3976[org.codehaus.groovy.ast.expr.VariableExpression@5ef8df1e[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@27cf3151[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@127e70c5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5910de75[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4108fa66[org.codehaus.groovy.ast.expr.GStringExpression@1f130eaf[strings: [ConstantExpression[], ConstantExpression[.markDups_metrics.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7e0aadd0[object: org.codehaus.groovy.ast.expr.VariableExpression@21362712[variable: bam_markduplicates] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27eb3298[org.codehaus.groovy.ast.expr.VariableExpression@200a26bc[variable: picard_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@bc57b40[expression:org.codehaus.groovy.ast.expr.GStringExpression@1b5bc39d[strings: [ConstantExpression[
    java -Xmx2g -jar $PICARD_HOME/picard.jar MarkDuplicates \
        INPUT=], ConstantExpression[ \
        OUTPUT=], ConstantExpression[.markDups.bam \
        METRICS_FILE=], ConstantExpression[.markDups_metrics.txt \
        REMOVE_DUPLICATES=false \
        ASSUME_SORTED=true \
        PROGRAM_RECORD_ID='null' \
        VALIDATION_STRINGENCY=LENIENT

    # Print version number to standard out
    echo "File name: ], ConstantExpression[ Picard version "$(java -Xmx2g -jar $PICARD_HOME/picard.jar  MarkDuplicates --version 2>&1)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@655a5d9c[variable: bam_markduplicates], org.codehaus.groovy.ast.expr.PropertyExpression@1494b84d[object: org.codehaus.groovy.ast.expr.VariableExpression@34abdee4[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@71a9b4c7[object: org.codehaus.groovy.ast.expr.VariableExpression@4628b1d3[variable: bam_markduplicates] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@77cf3f8b[variable: bam_markduplicates]]]]] }]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@aa22f1c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@55e7a35c[org.codehaus.groovy.ast.expr.VariableExpression@37cd92d6[variable: bam_markduplicates]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4263b080[object: org.codehaus.groovy.ast.expr.MethodCallExpression@2af616d3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71f67a79[org.codehaus.groovy.ast.expr.GStringExpression@3deb2326[strings: [ConstantExpression[], ConstantExpression[.markDups.bam]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@21ca139cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@226f885f[org.codehaus.groovy.ast.stmt.ExpressionStatement@2cd2c8fe[expression:org.codehaus.groovy.ast.expr.PropertyExpression@62d363ab[object: org.codehaus.groovy.ast.expr.VariableExpression@7889a1ac[variable: bam_markduplicates] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aee3976[org.codehaus.groovy.ast.expr.VariableExpression@5ef8df1e[variable: bam_md]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2af616d3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71f67a79[org.codehaus.groovy.ast.expr.GStringExpression@3deb2326[strings: [ConstantExpression[], ConstantExpression[.markDups.bam]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@21ca139cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@226f885f[org.codehaus.groovy.ast.stmt.ExpressionStatement@2cd2c8fe[expression:org.codehaus.groovy.ast.expr.PropertyExpression@62d363ab[object: org.codehaus.groovy.ast.expr.VariableExpression@7889a1ac[variable: bam_markduplicates] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@127e70c5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5910de75[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4108fa66[org.codehaus.groovy.ast.expr.GStringExpression@1f130eaf[strings: [ConstantExpression[], ConstantExpression[.markDups_metrics.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@7d61eccfnull{ org.codehaus.groovy.ast.stmt.BlockStatement@cc6460c[org.codehaus.groovy.ast.stmt.ExpressionStatement@52350abb[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7e0aadd0[object: org.codehaus.groovy.ast.expr.VariableExpression@21362712[variable: bam_markduplicates] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27eb3298[org.codehaus.groovy.ast.expr.VariableExpression@200a26bc[variable: picard_results]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5910de75[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4108fa66[org.codehaus.groovy.ast.expr.GStringExpression@1f130eaf[strings: [ConstantExpression[], ConstantExpression[.markDups_metrics.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@7d61eccfnull{ org.codehaus.groovy.ast.stmt.BlockStatement@cc6460c[org.codehaus.groovy.ast.stmt.ExpressionStatement@52350abb[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7e0aadd0[object: org.codehaus.groovy.ast.expr.VariableExpression@21362712[variable: bam_markduplicates] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.631 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.634 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@681aad3b[org.codehaus.groovy.ast.expr.MethodCallExpression@1a6f2363[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[dupradar] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2427e004[org.codehaus.groovy.ast.expr.ClosureExpression@5ebd56e9[]{ org.codehaus.groovy.ast.stmt.BlockStatement@63f34b70[org.codehaus.groovy.ast.stmt.ExpressionStatement@641856[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1b58ff9e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f66e802[org.codehaus.groovy.ast.expr.GStringExpression@56b78e55[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76318a7d[object: org.codehaus.groovy.ast.expr.VariableExpression@2a492f2a[variable: bam_md] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3277e499[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@585811a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@22c01ab0[org.codehaus.groovy.ast.expr.MapExpression@411341bd[org.codehaus.groovy.ast.expr.MapEntryExpression@4c4d362a(key: ConstantExpression[pattern], value: ConstantExpression[*.{pdf,txt}]), org.codehaus.groovy.ast.expr.MapEntryExpression@5400db36(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@76b74e9c[strings: [ConstantExpression[], ConstantExpression[/dupradar]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d72f75e[object: org.codehaus.groovy.ast.expr.VariableExpression@8ab78bc[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5aa0dbf4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@16afbd92[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2c5d601e[org.codehaus.groovy.ast.expr.ClosureExpression@7fe083b1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@23c388c2[org.codehaus.groovy.ast.stmt.ExpressionStatement@486be205[expression:org.codehaus.groovy.ast.expr.BinaryExpression@f713686[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@74f7d1d2[org.codehaus.groovy.ast.expr.BooleanExpression@4b4dd216 ? org.codehaus.groovy.ast.expr.PropertyExpression@5ca17ab0[object: org.codehaus.groovy.ast.expr.VariableExpression@5a62b2a4[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1051817b[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 622:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@35293c05[object: org.codehaus.groovy.ast.expr.VariableExpression@620aa4ea[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2db2dd9d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3174cb09[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4d411036[org.codehaus.groovy.ast.expr.ClosureExpression@7adbd080[]{ org.codehaus.groovy.ast.stmt.BlockStatement@41beb473[org.codehaus.groovy.ast.stmt.ExpressionStatement@560513ce[expression:org.codehaus.groovy.ast.expr.BinaryExpression@13006998[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37fbe4a8[org.codehaus.groovy.ast.expr.BooleanExpression@352c308 ? org.codehaus.groovy.ast.expr.PropertyExpression@7d373bcf[object: org.codehaus.groovy.ast.expr.VariableExpression@6d6bc158[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5dda6f9[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 623:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@10027fc9[object: org.codehaus.groovy.ast.expr.VariableExpression@54afd745[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@677dbd89[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@fff25f1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c00fff0[org.codehaus.groovy.ast.expr.VariableExpression@263f04ca[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ca47471[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5a021cb9[object: org.codehaus.groovy.ast.expr.MethodCallExpression@51768776[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f31c0c6[org.codehaus.groovy.ast.expr.VariableExpression@b93aad[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a9419d7[org.codehaus.groovy.ast.expr.VariableExpression@2f3c6ac4[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e8ab815[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67af833b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@d1f74b8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41394595[ConstantExpression[*.{pdf,txt}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a0807b7[org.codehaus.groovy.ast.expr.VariableExpression@21a5fd96[variable: dupradar_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5769e7ae[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@5c77053b[org.codehaus.groovy.ast.expr.VariableExpression@26b894bd[variable: paired]("=" at 633:5:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@287f94b1[org.codehaus.groovy.ast.expr.BooleanExpression@30b34287 ? ConstantExpression[FALSE] : ConstantExpression[TRUE]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5489c777[expression:org.codehaus.groovy.ast.expr.GStringExpression@3676ac27[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install dupRadar package
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("dupRadar")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("dupRadar", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("dupRadar")
    }

    # Duplicate stats
    stranded <- 2
    threads <- 8
    dm <- analyzeDuprates("], ConstantExpression[", "], ConstantExpression[", stranded, ], ConstantExpression[, threads)
    write.table(dm, file=paste("], ConstantExpression[", "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")

    # 2D density scatter plot
    pdf(paste0("], ConstantExpression[", "_duprateExpDens.pdf"))
    duprateExpDensPlot(DupMat=dm)
    title("Density scatter plot")
    mtext("], ConstantExpression[", side=3)
    dev.off()
    fit <- duprateExpFit(DupMat=dm)
    cat(
      paste("- dupRadar Int (duprate at low read counts):", fit$intercept),
      paste("- dupRadar Sl (progression of the duplication rate):", fit$slope),
      fill=TRUE, labels="], ConstantExpression[",
      file=paste0("], ConstantExpression[", "_intercept_slope.txt"), append=FALSE
    )

    # Get numbers from dupRadar GLM
    curve_x <- sort(log10(dm$RPK))
    curve_y = 100*predict(fit$glm,data.frame(x=curve_x),type="response")
    # Remove all of the infinite values
    infs = which(curve_x %in% c(-Inf,Inf))
    curve_x = curve_x[-infs]
    curve_y = curve_y[-infs]
    # Reduce number of data points
    curve_x <- curve_x[seq(1, length(curve_x), 10)]
    curve_y <- curve_y[seq(1, length(curve_y), 10)]
    # Convert x values back to real counts
    curve_x = 10^curve_x
    # Write to file
    write.table(
      cbind(curve_x, curve_y),
      file=paste0("], ConstantExpression[", "_duprateExpDensCurve.txt"),
      quote=FALSE, row.names=FALSE
    )

    # Distribution of expression box plot
    pdf(paste0("], ConstantExpression[", "_duprateExpBoxplot.pdf"))
    duprateExpBoxplot(DupMat=dm)
    title("Percent Duplication by Expression")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Distribution of RPK values per gene
    pdf(paste0("], ConstantExpression[", "_expressionHist.pdf"))
    expressionHist(DupMat=dm)
    title("Distribution of RPK values per gene")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Printing sessioninfo to standard out
    print("], ConstantExpression[")
    citation("dupRadar")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62f87c44[object: org.codehaus.groovy.ast.expr.VariableExpression@48f5bde6[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@525d79f0[object: org.codehaus.groovy.ast.expr.VariableExpression@5149f008[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.VariableExpression@7072bc39[variable: bam_md], org.codehaus.groovy.ast.expr.VariableExpression@158d255c[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@2ca65ce4[variable: paired], org.codehaus.groovy.ast.expr.PropertyExpression@327120c8[object: org.codehaus.groovy.ast.expr.VariableExpression@5707c1cb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2b5cb9b2[object: org.codehaus.groovy.ast.expr.VariableExpression@35038141[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@ecf9049[object: org.codehaus.groovy.ast.expr.VariableExpression@672f11c2[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2970a5bc[object: org.codehaus.groovy.ast.expr.VariableExpression@50305a[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@72efb5c1[object: org.codehaus.groovy.ast.expr.VariableExpression@6d511b5f[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@41200e0c[object: org.codehaus.groovy.ast.expr.VariableExpression@40f33492[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@4fbdc0f0[object: org.codehaus.groovy.ast.expr.VariableExpression@2ad3a1bb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@6bc28a83[object: org.codehaus.groovy.ast.expr.VariableExpression@324c64cd[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@13579834[object: org.codehaus.groovy.ast.expr.VariableExpression@24be2d9c[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@5bd73d1a[object: org.codehaus.groovy.ast.expr.VariableExpression@aec50a1[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2555fff0[object: org.codehaus.groovy.ast.expr.VariableExpression@70d2e40b[variable: bam_md] property: ConstantExpression[baseName]]]]]] }]]]
Nov-14 16:09:26.634 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: dupradar with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@2427e004[org.codehaus.groovy.ast.expr.ClosureExpression@5ebd56e9[]{ org.codehaus.groovy.ast.stmt.BlockStatement@63f34b70[org.codehaus.groovy.ast.stmt.ExpressionStatement@641856[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1b58ff9e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f66e802[org.codehaus.groovy.ast.expr.GStringExpression@56b78e55[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76318a7d[object: org.codehaus.groovy.ast.expr.VariableExpression@2a492f2a[variable: bam_md] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3277e499[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@585811a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@22c01ab0[org.codehaus.groovy.ast.expr.MapExpression@411341bd[org.codehaus.groovy.ast.expr.MapEntryExpression@4c4d362a(key: ConstantExpression[pattern], value: ConstantExpression[*.{pdf,txt}]), org.codehaus.groovy.ast.expr.MapEntryExpression@5400db36(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@76b74e9c[strings: [ConstantExpression[], ConstantExpression[/dupradar]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d72f75e[object: org.codehaus.groovy.ast.expr.VariableExpression@8ab78bc[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5aa0dbf4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@16afbd92[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2c5d601e[org.codehaus.groovy.ast.expr.ClosureExpression@7fe083b1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@23c388c2[org.codehaus.groovy.ast.stmt.ExpressionStatement@486be205[expression:org.codehaus.groovy.ast.expr.BinaryExpression@f713686[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@74f7d1d2[org.codehaus.groovy.ast.expr.BooleanExpression@4b4dd216 ? org.codehaus.groovy.ast.expr.PropertyExpression@5ca17ab0[object: org.codehaus.groovy.ast.expr.VariableExpression@5a62b2a4[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1051817b[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 622:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@35293c05[object: org.codehaus.groovy.ast.expr.VariableExpression@620aa4ea[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2db2dd9d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3174cb09[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4d411036[org.codehaus.groovy.ast.expr.ClosureExpression@7adbd080[]{ org.codehaus.groovy.ast.stmt.BlockStatement@41beb473[org.codehaus.groovy.ast.stmt.ExpressionStatement@560513ce[expression:org.codehaus.groovy.ast.expr.BinaryExpression@13006998[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37fbe4a8[org.codehaus.groovy.ast.expr.BooleanExpression@352c308 ? org.codehaus.groovy.ast.expr.PropertyExpression@7d373bcf[object: org.codehaus.groovy.ast.expr.VariableExpression@6d6bc158[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5dda6f9[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 623:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@10027fc9[object: org.codehaus.groovy.ast.expr.VariableExpression@54afd745[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@677dbd89[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@fff25f1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c00fff0[org.codehaus.groovy.ast.expr.VariableExpression@263f04ca[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ca47471[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5a021cb9[object: org.codehaus.groovy.ast.expr.MethodCallExpression@51768776[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f31c0c6[org.codehaus.groovy.ast.expr.VariableExpression@b93aad[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a9419d7[org.codehaus.groovy.ast.expr.VariableExpression@2f3c6ac4[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e8ab815[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67af833b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@d1f74b8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41394595[ConstantExpression[*.{pdf,txt}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a0807b7[org.codehaus.groovy.ast.expr.VariableExpression@21a5fd96[variable: dupradar_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5769e7ae[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@5c77053b[org.codehaus.groovy.ast.expr.VariableExpression@26b894bd[variable: paired]("=" at 633:5:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@287f94b1[org.codehaus.groovy.ast.expr.BooleanExpression@30b34287 ? ConstantExpression[FALSE] : ConstantExpression[TRUE]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5489c777[expression:org.codehaus.groovy.ast.expr.GStringExpression@3676ac27[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install dupRadar package
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("dupRadar")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("dupRadar", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("dupRadar")
    }

    # Duplicate stats
    stranded <- 2
    threads <- 8
    dm <- analyzeDuprates("], ConstantExpression[", "], ConstantExpression[", stranded, ], ConstantExpression[, threads)
    write.table(dm, file=paste("], ConstantExpression[", "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")

    # 2D density scatter plot
    pdf(paste0("], ConstantExpression[", "_duprateExpDens.pdf"))
    duprateExpDensPlot(DupMat=dm)
    title("Density scatter plot")
    mtext("], ConstantExpression[", side=3)
    dev.off()
    fit <- duprateExpFit(DupMat=dm)
    cat(
      paste("- dupRadar Int (duprate at low read counts):", fit$intercept),
      paste("- dupRadar Sl (progression of the duplication rate):", fit$slope),
      fill=TRUE, labels="], ConstantExpression[",
      file=paste0("], ConstantExpression[", "_intercept_slope.txt"), append=FALSE
    )

    # Get numbers from dupRadar GLM
    curve_x <- sort(log10(dm$RPK))
    curve_y = 100*predict(fit$glm,data.frame(x=curve_x),type="response")
    # Remove all of the infinite values
    infs = which(curve_x %in% c(-Inf,Inf))
    curve_x = curve_x[-infs]
    curve_y = curve_y[-infs]
    # Reduce number of data points
    curve_x <- curve_x[seq(1, length(curve_x), 10)]
    curve_y <- curve_y[seq(1, length(curve_y), 10)]
    # Convert x values back to real counts
    curve_x = 10^curve_x
    # Write to file
    write.table(
      cbind(curve_x, curve_y),
      file=paste0("], ConstantExpression[", "_duprateExpDensCurve.txt"),
      quote=FALSE, row.names=FALSE
    )

    # Distribution of expression box plot
    pdf(paste0("], ConstantExpression[", "_duprateExpBoxplot.pdf"))
    duprateExpBoxplot(DupMat=dm)
    title("Percent Duplication by Expression")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Distribution of RPK values per gene
    pdf(paste0("], ConstantExpression[", "_expressionHist.pdf"))
    expressionHist(DupMat=dm)
    title("Distribution of RPK values per gene")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Printing sessioninfo to standard out
    print("], ConstantExpression[")
    citation("dupRadar")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62f87c44[object: org.codehaus.groovy.ast.expr.VariableExpression@48f5bde6[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@525d79f0[object: org.codehaus.groovy.ast.expr.VariableExpression@5149f008[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.VariableExpression@7072bc39[variable: bam_md], org.codehaus.groovy.ast.expr.VariableExpression@158d255c[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@2ca65ce4[variable: paired], org.codehaus.groovy.ast.expr.PropertyExpression@327120c8[object: org.codehaus.groovy.ast.expr.VariableExpression@5707c1cb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2b5cb9b2[object: org.codehaus.groovy.ast.expr.VariableExpression@35038141[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@ecf9049[object: org.codehaus.groovy.ast.expr.VariableExpression@672f11c2[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2970a5bc[object: org.codehaus.groovy.ast.expr.VariableExpression@50305a[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@72efb5c1[object: org.codehaus.groovy.ast.expr.VariableExpression@6d511b5f[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@41200e0c[object: org.codehaus.groovy.ast.expr.VariableExpression@40f33492[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@4fbdc0f0[object: org.codehaus.groovy.ast.expr.VariableExpression@2ad3a1bb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@6bc28a83[object: org.codehaus.groovy.ast.expr.VariableExpression@324c64cd[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@13579834[object: org.codehaus.groovy.ast.expr.VariableExpression@24be2d9c[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@5bd73d1a[object: org.codehaus.groovy.ast.expr.VariableExpression@aec50a1[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2555fff0[object: org.codehaus.groovy.ast.expr.VariableExpression@70d2e40b[variable: bam_md] property: ConstantExpression[baseName]]]]]] }]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@120f38e6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2427e004[ConstantExpression[dupradar], org.codehaus.groovy.ast.expr.ClosureExpression@5ebd56e9[]{ org.codehaus.groovy.ast.stmt.BlockStatement@63f34b70[org.codehaus.groovy.ast.stmt.ExpressionStatement@641856[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1b58ff9e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2f66e802[org.codehaus.groovy.ast.expr.GStringExpression@56b78e55[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@76318a7d[object: org.codehaus.groovy.ast.expr.VariableExpression@2a492f2a[variable: bam_md] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3277e499[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@585811a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@22c01ab0[org.codehaus.groovy.ast.expr.MapExpression@411341bd[org.codehaus.groovy.ast.expr.MapEntryExpression@4c4d362a(key: ConstantExpression[pattern], value: ConstantExpression[*.{pdf,txt}]), org.codehaus.groovy.ast.expr.MapEntryExpression@5400db36(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@76b74e9c[strings: [ConstantExpression[], ConstantExpression[/dupradar]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d72f75e[object: org.codehaus.groovy.ast.expr.VariableExpression@8ab78bc[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5aa0dbf4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@16afbd92[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2c5d601e[org.codehaus.groovy.ast.expr.ClosureExpression@7fe083b1[]{ org.codehaus.groovy.ast.stmt.BlockStatement@23c388c2[org.codehaus.groovy.ast.stmt.ExpressionStatement@486be205[expression:org.codehaus.groovy.ast.expr.BinaryExpression@f713686[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@74f7d1d2[org.codehaus.groovy.ast.expr.BooleanExpression@4b4dd216 ? org.codehaus.groovy.ast.expr.PropertyExpression@5ca17ab0[object: org.codehaus.groovy.ast.expr.VariableExpression@5a62b2a4[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1051817b[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 622:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@35293c05[object: org.codehaus.groovy.ast.expr.VariableExpression@620aa4ea[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2db2dd9d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3174cb09[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4d411036[org.codehaus.groovy.ast.expr.ClosureExpression@7adbd080[]{ org.codehaus.groovy.ast.stmt.BlockStatement@41beb473[org.codehaus.groovy.ast.stmt.ExpressionStatement@560513ce[expression:org.codehaus.groovy.ast.expr.BinaryExpression@13006998[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@37fbe4a8[org.codehaus.groovy.ast.expr.BooleanExpression@352c308 ? org.codehaus.groovy.ast.expr.PropertyExpression@7d373bcf[object: org.codehaus.groovy.ast.expr.VariableExpression@6d6bc158[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@5dda6f9[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 623:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@10027fc9[object: org.codehaus.groovy.ast.expr.VariableExpression@54afd745[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@677dbd89[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@fff25f1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c00fff0[org.codehaus.groovy.ast.expr.VariableExpression@263f04ca[variable: bam_md]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2ca47471[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5a021cb9[object: org.codehaus.groovy.ast.expr.MethodCallExpression@51768776[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f31c0c6[org.codehaus.groovy.ast.expr.VariableExpression@b93aad[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a9419d7[org.codehaus.groovy.ast.expr.VariableExpression@2f3c6ac4[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2e8ab815[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@67af833b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@d1f74b8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41394595[ConstantExpression[*.{pdf,txt}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a0807b7[org.codehaus.groovy.ast.expr.VariableExpression@21a5fd96[variable: dupradar_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5769e7ae[expression:org.codehaus.groovy.ast.expr.DeclarationExpression@5c77053b[org.codehaus.groovy.ast.expr.VariableExpression@26b894bd[variable: paired]("=" at 633:5:  "=" )org.codehaus.groovy.ast.expr.TernaryExpression@287f94b1[org.codehaus.groovy.ast.expr.BooleanExpression@30b34287 ? ConstantExpression[FALSE] : ConstantExpression[TRUE]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5489c777[expression:org.codehaus.groovy.ast.expr.GStringExpression@3676ac27[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install dupRadar package
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("dupRadar")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("dupRadar", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("dupRadar")
    }

    # Duplicate stats
    stranded <- 2
    threads <- 8
    dm <- analyzeDuprates("], ConstantExpression[", "], ConstantExpression[", stranded, ], ConstantExpression[, threads)
    write.table(dm, file=paste("], ConstantExpression[", "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")

    # 2D density scatter plot
    pdf(paste0("], ConstantExpression[", "_duprateExpDens.pdf"))
    duprateExpDensPlot(DupMat=dm)
    title("Density scatter plot")
    mtext("], ConstantExpression[", side=3)
    dev.off()
    fit <- duprateExpFit(DupMat=dm)
    cat(
      paste("- dupRadar Int (duprate at low read counts):", fit$intercept),
      paste("- dupRadar Sl (progression of the duplication rate):", fit$slope),
      fill=TRUE, labels="], ConstantExpression[",
      file=paste0("], ConstantExpression[", "_intercept_slope.txt"), append=FALSE
    )

    # Get numbers from dupRadar GLM
    curve_x <- sort(log10(dm$RPK))
    curve_y = 100*predict(fit$glm,data.frame(x=curve_x),type="response")
    # Remove all of the infinite values
    infs = which(curve_x %in% c(-Inf,Inf))
    curve_x = curve_x[-infs]
    curve_y = curve_y[-infs]
    # Reduce number of data points
    curve_x <- curve_x[seq(1, length(curve_x), 10)]
    curve_y <- curve_y[seq(1, length(curve_y), 10)]
    # Convert x values back to real counts
    curve_x = 10^curve_x
    # Write to file
    write.table(
      cbind(curve_x, curve_y),
      file=paste0("], ConstantExpression[", "_duprateExpDensCurve.txt"),
      quote=FALSE, row.names=FALSE
    )

    # Distribution of expression box plot
    pdf(paste0("], ConstantExpression[", "_duprateExpBoxplot.pdf"))
    duprateExpBoxplot(DupMat=dm)
    title("Percent Duplication by Expression")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Distribution of RPK values per gene
    pdf(paste0("], ConstantExpression[", "_expressionHist.pdf"))
    expressionHist(DupMat=dm)
    title("Distribution of RPK values per gene")
    mtext("], ConstantExpression[", side=3)
    dev.off()

    # Printing sessioninfo to standard out
    print("], ConstantExpression[")
    citation("dupRadar")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@62f87c44[object: org.codehaus.groovy.ast.expr.VariableExpression@48f5bde6[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@525d79f0[object: org.codehaus.groovy.ast.expr.VariableExpression@5149f008[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.VariableExpression@7072bc39[variable: bam_md], org.codehaus.groovy.ast.expr.VariableExpression@158d255c[variable: gtf], org.codehaus.groovy.ast.expr.VariableExpression@2ca65ce4[variable: paired], org.codehaus.groovy.ast.expr.PropertyExpression@327120c8[object: org.codehaus.groovy.ast.expr.VariableExpression@5707c1cb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2b5cb9b2[object: org.codehaus.groovy.ast.expr.VariableExpression@35038141[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@ecf9049[object: org.codehaus.groovy.ast.expr.VariableExpression@672f11c2[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2970a5bc[object: org.codehaus.groovy.ast.expr.VariableExpression@50305a[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@72efb5c1[object: org.codehaus.groovy.ast.expr.VariableExpression@6d511b5f[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@41200e0c[object: org.codehaus.groovy.ast.expr.VariableExpression@40f33492[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@4fbdc0f0[object: org.codehaus.groovy.ast.expr.VariableExpression@2ad3a1bb[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@6bc28a83[object: org.codehaus.groovy.ast.expr.VariableExpression@324c64cd[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@13579834[object: org.codehaus.groovy.ast.expr.VariableExpression@24be2d9c[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@5bd73d1a[object: org.codehaus.groovy.ast.expr.VariableExpression@aec50a1[variable: bam_md] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@2555fff0[object: org.codehaus.groovy.ast.expr.VariableExpression@70d2e40b[variable: bam_md] property: ConstantExpression[baseName]]]]]] }]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@fff25f1[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c00fff0[org.codehaus.groovy.ast.expr.VariableExpression@263f04ca[variable: bam_md]]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5a021cb9[object: org.codehaus.groovy.ast.expr.MethodCallExpression@51768776[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f31c0c6[org.codehaus.groovy.ast.expr.VariableExpression@b93aad[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4a9419d7[org.codehaus.groovy.ast.expr.VariableExpression@2f3c6ac4[variable: gtf]]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@51768776[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@f31c0c6[org.codehaus.groovy.ast.expr.VariableExpression@b93aad[variable: gtf]]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@67af833b[object: org.codehaus.groovy.ast.expr.MethodCallExpression@d1f74b8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41394595[ConstantExpression[*.{pdf,txt}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3a0807b7[org.codehaus.groovy.ast.expr.VariableExpression@21a5fd96[variable: dupradar_results]]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@d1f74b8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41394595[ConstantExpression[*.{pdf,txt}]]]
Nov-14 16:09:26.635 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.639 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@7a0e1b5e[org.codehaus.groovy.ast.expr.MethodCallExpression@702ed190[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[featureCounts] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@173b9122[org.codehaus.groovy.ast.expr.ClosureExpression@7c18432b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7646731d[org.codehaus.groovy.ast.stmt.ExpressionStatement@70e29e14[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b1bb3ab[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a4bef8[org.codehaus.groovy.ast.expr.GStringExpression@40bffbca[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2449cff7[variable: bam_featurecounts]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42a9a63e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62da83ed[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d8445d7[org.codehaus.groovy.ast.expr.MapExpression@37d80fe7[org.codehaus.groovy.ast.expr.MapEntryExpression@384fc774(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@e3cee7b[strings: [ConstantExpression[], ConstantExpression[/featureCounts]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71e9a896[object: org.codehaus.groovy.ast.expr.VariableExpression@6b9267b[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@408b35bf[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29ad44e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@15bcf458[org.codehaus.groovy.ast.expr.ClosureExpression@5af9926a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@43c67247[org.codehaus.groovy.ast.stmt.ExpressionStatement@fac80[expression:org.codehaus.groovy.ast.expr.BinaryExpression@726386ed[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@649f2009[org.codehaus.groovy.ast.expr.BooleanExpression@14bb2297 ? org.codehaus.groovy.ast.expr.PropertyExpression@69adf72c[object: org.codehaus.groovy.ast.expr.VariableExpression@797501a[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1a15b789[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 714:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@57f791c6[object: org.codehaus.groovy.ast.expr.VariableExpression@51650883[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6c4f9535[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5bd1ceca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30c31dd7[org.codehaus.groovy.ast.expr.ClosureExpression@499b2a5c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@596df867[org.codehaus.groovy.ast.stmt.ExpressionStatement@c1fca1e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@241a53ef[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@344344fa[org.codehaus.groovy.ast.expr.BooleanExpression@2db2cd5 ? org.codehaus.groovy.ast.expr.PropertyExpression@70e659aa[object: org.codehaus.groovy.ast.expr.VariableExpression@615f972[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@285f09de[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 715:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@73393584[object: org.codehaus.groovy.ast.expr.VariableExpression@31500940[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1827a871[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@48e64352[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7249dadf[org.codehaus.groovy.ast.expr.VariableExpression@4362d7df[variable: bam_featurecounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66238be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c25b8a7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@200606de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@750fe12e[org.codehaus.groovy.ast.expr.VariableExpression@f8908f6[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3e587920[org.codehaus.groovy.ast.expr.VariableExpression@2ef8a8c3[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@24f43aa3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@63fd4873[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e11bc55[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7544a1e4[org.codehaus.groovy.ast.expr.GStringExpression@70e0accd[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7957dc72[object: org.codehaus.groovy.ast.expr.VariableExpression@6ab72419[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aacf32a[org.codehaus.groovy.ast.expr.VariableExpression@4fdfa676[variable: geneCounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@82c57b3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5be82d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@600b0b7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@345e5a17[org.codehaus.groovy.ast.expr.GStringExpression@5ea502e0[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt.summary]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@443dbe42[object: org.codehaus.groovy.ast.expr.VariableExpression@473b3b7a[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1734f68[org.codehaus.groovy.ast.expr.VariableExpression@77b7ffa4[variable: featureCounts_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5ed190be[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@402f80f5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5bbc9f97[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@133e019b[org.codehaus.groovy.ast.expr.GStringExpression@41382722[strings: [ConstantExpression[], ConstantExpression[_biotype_counts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7dac3fd8[object: org.codehaus.groovy.ast.expr.VariableExpression@425357dd[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2102a4d5[org.codehaus.groovy.ast.expr.VariableExpression@210386e0[variable: featureCounts_biotype]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d4d3fe7[expression:org.codehaus.groovy.ast.expr.GStringExpression@65f87a2c[strings: [ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_id -o ], ConstantExpression[_gene.featureCounts.txt -p -s 2 ], ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_biotype -o ], ConstantExpression[_biotype.featureCounts.txt -p -s 2 ], ConstantExpression[
    cut -f 1,7 ], ConstantExpression[_biotype.featureCounts.txt > ], ConstantExpression[_biotype_counts.txt
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51684e4a[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6ce1f601[object: org.codehaus.groovy.ast.expr.VariableExpression@38875e7d[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@1e886a5b[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@d816dde[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6e33c391[object: org.codehaus.groovy.ast.expr.VariableExpression@6c451c9c[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@31c269fd[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.PropertyExpression@372b0d86[object: org.codehaus.groovy.ast.expr.VariableExpression@47747fb9[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@3113a37[object: org.codehaus.groovy.ast.expr.VariableExpression@213e3629[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] }]]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: featureCounts with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@173b9122[org.codehaus.groovy.ast.expr.ClosureExpression@7c18432b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7646731d[org.codehaus.groovy.ast.stmt.ExpressionStatement@70e29e14[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b1bb3ab[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a4bef8[org.codehaus.groovy.ast.expr.GStringExpression@40bffbca[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2449cff7[variable: bam_featurecounts]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42a9a63e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62da83ed[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d8445d7[org.codehaus.groovy.ast.expr.MapExpression@37d80fe7[org.codehaus.groovy.ast.expr.MapEntryExpression@384fc774(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@e3cee7b[strings: [ConstantExpression[], ConstantExpression[/featureCounts]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71e9a896[object: org.codehaus.groovy.ast.expr.VariableExpression@6b9267b[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@408b35bf[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29ad44e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@15bcf458[org.codehaus.groovy.ast.expr.ClosureExpression@5af9926a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@43c67247[org.codehaus.groovy.ast.stmt.ExpressionStatement@fac80[expression:org.codehaus.groovy.ast.expr.BinaryExpression@726386ed[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@649f2009[org.codehaus.groovy.ast.expr.BooleanExpression@14bb2297 ? org.codehaus.groovy.ast.expr.PropertyExpression@69adf72c[object: org.codehaus.groovy.ast.expr.VariableExpression@797501a[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1a15b789[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 714:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@57f791c6[object: org.codehaus.groovy.ast.expr.VariableExpression@51650883[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6c4f9535[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5bd1ceca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30c31dd7[org.codehaus.groovy.ast.expr.ClosureExpression@499b2a5c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@596df867[org.codehaus.groovy.ast.stmt.ExpressionStatement@c1fca1e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@241a53ef[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@344344fa[org.codehaus.groovy.ast.expr.BooleanExpression@2db2cd5 ? org.codehaus.groovy.ast.expr.PropertyExpression@70e659aa[object: org.codehaus.groovy.ast.expr.VariableExpression@615f972[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@285f09de[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 715:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@73393584[object: org.codehaus.groovy.ast.expr.VariableExpression@31500940[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1827a871[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@48e64352[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7249dadf[org.codehaus.groovy.ast.expr.VariableExpression@4362d7df[variable: bam_featurecounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66238be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c25b8a7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@200606de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@750fe12e[org.codehaus.groovy.ast.expr.VariableExpression@f8908f6[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3e587920[org.codehaus.groovy.ast.expr.VariableExpression@2ef8a8c3[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@24f43aa3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@63fd4873[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e11bc55[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7544a1e4[org.codehaus.groovy.ast.expr.GStringExpression@70e0accd[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7957dc72[object: org.codehaus.groovy.ast.expr.VariableExpression@6ab72419[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aacf32a[org.codehaus.groovy.ast.expr.VariableExpression@4fdfa676[variable: geneCounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@82c57b3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5be82d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@600b0b7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@345e5a17[org.codehaus.groovy.ast.expr.GStringExpression@5ea502e0[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt.summary]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@443dbe42[object: org.codehaus.groovy.ast.expr.VariableExpression@473b3b7a[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1734f68[org.codehaus.groovy.ast.expr.VariableExpression@77b7ffa4[variable: featureCounts_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5ed190be[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@402f80f5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5bbc9f97[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@133e019b[org.codehaus.groovy.ast.expr.GStringExpression@41382722[strings: [ConstantExpression[], ConstantExpression[_biotype_counts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7dac3fd8[object: org.codehaus.groovy.ast.expr.VariableExpression@425357dd[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2102a4d5[org.codehaus.groovy.ast.expr.VariableExpression@210386e0[variable: featureCounts_biotype]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d4d3fe7[expression:org.codehaus.groovy.ast.expr.GStringExpression@65f87a2c[strings: [ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_id -o ], ConstantExpression[_gene.featureCounts.txt -p -s 2 ], ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_biotype -o ], ConstantExpression[_biotype.featureCounts.txt -p -s 2 ], ConstantExpression[
    cut -f 1,7 ], ConstantExpression[_biotype.featureCounts.txt > ], ConstantExpression[_biotype_counts.txt
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51684e4a[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6ce1f601[object: org.codehaus.groovy.ast.expr.VariableExpression@38875e7d[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@1e886a5b[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@d816dde[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6e33c391[object: org.codehaus.groovy.ast.expr.VariableExpression@6c451c9c[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@31c269fd[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.PropertyExpression@372b0d86[object: org.codehaus.groovy.ast.expr.VariableExpression@47747fb9[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@3113a37[object: org.codehaus.groovy.ast.expr.VariableExpression@213e3629[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] }]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@4e9658b5[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@173b9122[ConstantExpression[featureCounts], org.codehaus.groovy.ast.expr.ClosureExpression@7c18432b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@7646731d[org.codehaus.groovy.ast.stmt.ExpressionStatement@70e29e14[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3b1bb3ab[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a4bef8[org.codehaus.groovy.ast.expr.GStringExpression@40bffbca[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@2449cff7[variable: bam_featurecounts]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@42a9a63e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@62da83ed[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d8445d7[org.codehaus.groovy.ast.expr.MapExpression@37d80fe7[org.codehaus.groovy.ast.expr.MapEntryExpression@384fc774(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@e3cee7b[strings: [ConstantExpression[], ConstantExpression[/featureCounts]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@71e9a896[object: org.codehaus.groovy.ast.expr.VariableExpression@6b9267b[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@408b35bf[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@29ad44e3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@15bcf458[org.codehaus.groovy.ast.expr.ClosureExpression@5af9926a[]{ org.codehaus.groovy.ast.stmt.BlockStatement@43c67247[org.codehaus.groovy.ast.stmt.ExpressionStatement@fac80[expression:org.codehaus.groovy.ast.expr.BinaryExpression@726386ed[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@649f2009[org.codehaus.groovy.ast.expr.BooleanExpression@14bb2297 ? org.codehaus.groovy.ast.expr.PropertyExpression@69adf72c[object: org.codehaus.groovy.ast.expr.VariableExpression@797501a[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@1a15b789[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 714:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@57f791c6[object: org.codehaus.groovy.ast.expr.VariableExpression@51650883[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6c4f9535[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5bd1ceca[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@30c31dd7[org.codehaus.groovy.ast.expr.ClosureExpression@499b2a5c[]{ org.codehaus.groovy.ast.stmt.BlockStatement@596df867[org.codehaus.groovy.ast.stmt.ExpressionStatement@c1fca1e[expression:org.codehaus.groovy.ast.expr.BinaryExpression@241a53ef[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@344344fa[org.codehaus.groovy.ast.expr.BooleanExpression@2db2cd5 ? org.codehaus.groovy.ast.expr.PropertyExpression@70e659aa[object: org.codehaus.groovy.ast.expr.VariableExpression@615f972[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@285f09de[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 715:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@73393584[object: org.codehaus.groovy.ast.expr.VariableExpression@31500940[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1827a871[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@48e64352[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7249dadf[org.codehaus.groovy.ast.expr.VariableExpression@4362d7df[variable: bam_featurecounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@66238be2[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c25b8a7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@200606de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@750fe12e[org.codehaus.groovy.ast.expr.VariableExpression@f8908f6[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3e587920[org.codehaus.groovy.ast.expr.VariableExpression@2ef8a8c3[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@24f43aa3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@63fd4873[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e11bc55[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7544a1e4[org.codehaus.groovy.ast.expr.GStringExpression@70e0accd[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7957dc72[object: org.codehaus.groovy.ast.expr.VariableExpression@6ab72419[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aacf32a[org.codehaus.groovy.ast.expr.VariableExpression@4fdfa676[variable: geneCounts]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@82c57b3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@5be82d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@600b0b7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@345e5a17[org.codehaus.groovy.ast.expr.GStringExpression@5ea502e0[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt.summary]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@443dbe42[object: org.codehaus.groovy.ast.expr.VariableExpression@473b3b7a[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1734f68[org.codehaus.groovy.ast.expr.VariableExpression@77b7ffa4[variable: featureCounts_logs]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5ed190be[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@402f80f5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5bbc9f97[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@133e019b[org.codehaus.groovy.ast.expr.GStringExpression@41382722[strings: [ConstantExpression[], ConstantExpression[_biotype_counts.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@7dac3fd8[object: org.codehaus.groovy.ast.expr.VariableExpression@425357dd[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2102a4d5[org.codehaus.groovy.ast.expr.VariableExpression@210386e0[variable: featureCounts_biotype]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3d4d3fe7[expression:org.codehaus.groovy.ast.expr.GStringExpression@65f87a2c[strings: [ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_id -o ], ConstantExpression[_gene.featureCounts.txt -p -s 2 ], ConstantExpression[
    featureCounts -a ], ConstantExpression[ -g gene_biotype -o ], ConstantExpression[_biotype.featureCounts.txt -p -s 2 ], ConstantExpression[
    cut -f 1,7 ], ConstantExpression[_biotype.featureCounts.txt > ], ConstantExpression[_biotype_counts.txt
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51684e4a[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6ce1f601[object: org.codehaus.groovy.ast.expr.VariableExpression@38875e7d[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@1e886a5b[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.VariableExpression@d816dde[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@6e33c391[object: org.codehaus.groovy.ast.expr.VariableExpression@6c451c9c[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@31c269fd[variable: bam_featurecounts], org.codehaus.groovy.ast.expr.PropertyExpression@372b0d86[object: org.codehaus.groovy.ast.expr.VariableExpression@47747fb9[variable: bam_featurecounts] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.PropertyExpression@3113a37[object: org.codehaus.groovy.ast.expr.VariableExpression@213e3629[variable: bam_featurecounts] property: ConstantExpression[baseName]]]]]] }]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@48e64352[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7249dadf[org.codehaus.groovy.ast.expr.VariableExpression@4362d7df[variable: bam_featurecounts]]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1c25b8a7[object: org.codehaus.groovy.ast.expr.MethodCallExpression@200606de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@750fe12e[org.codehaus.groovy.ast.expr.VariableExpression@f8908f6[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3e587920[org.codehaus.groovy.ast.expr.VariableExpression@2ef8a8c3[variable: gtf]]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@200606de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@750fe12e[org.codehaus.groovy.ast.expr.VariableExpression@f8908f6[variable: gtf]]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@63fd4873[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e11bc55[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7544a1e4[org.codehaus.groovy.ast.expr.GStringExpression@70e0accd[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@2a7b6f69null{ org.codehaus.groovy.ast.stmt.BlockStatement@20312893[org.codehaus.groovy.ast.stmt.ExpressionStatement@70eecdc2[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7957dc72[object: org.codehaus.groovy.ast.expr.VariableExpression@6ab72419[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3aacf32a[org.codehaus.groovy.ast.expr.VariableExpression@4fdfa676[variable: geneCounts]]]
Nov-14 16:09:26.640 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1e11bc55[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7544a1e4[org.codehaus.groovy.ast.expr.GStringExpression@70e0accd[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@2a7b6f69null{ org.codehaus.groovy.ast.stmt.BlockStatement@20312893[org.codehaus.groovy.ast.stmt.ExpressionStatement@70eecdc2[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7957dc72[object: org.codehaus.groovy.ast.expr.VariableExpression@6ab72419[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5be82d43[object: org.codehaus.groovy.ast.expr.MethodCallExpression@600b0b7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@345e5a17[org.codehaus.groovy.ast.expr.GStringExpression@5ea502e0[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt.summary]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@7db0565cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@54ec8cc9[org.codehaus.groovy.ast.stmt.ExpressionStatement@52eacb4b[expression:org.codehaus.groovy.ast.expr.PropertyExpression@443dbe42[object: org.codehaus.groovy.ast.expr.VariableExpression@473b3b7a[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1734f68[org.codehaus.groovy.ast.expr.VariableExpression@77b7ffa4[variable: featureCounts_logs]]]
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@600b0b7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@345e5a17[org.codehaus.groovy.ast.expr.GStringExpression@5ea502e0[strings: [ConstantExpression[], ConstantExpression[_gene.featureCounts.txt.summary]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@7db0565cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@54ec8cc9[org.codehaus.groovy.ast.stmt.ExpressionStatement@52eacb4b[expression:org.codehaus.groovy.ast.expr.PropertyExpression@443dbe42[object: org.codehaus.groovy.ast.expr.VariableExpression@473b3b7a[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@402f80f5[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5bbc9f97[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@133e019b[org.codehaus.groovy.ast.expr.GStringExpression@41382722[strings: [ConstantExpression[], ConstantExpression[_biotype_counts.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@5528a42cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@2a551a63[org.codehaus.groovy.ast.stmt.ExpressionStatement@1a6f5124[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7dac3fd8[object: org.codehaus.groovy.ast.expr.VariableExpression@425357dd[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2102a4d5[org.codehaus.groovy.ast.expr.VariableExpression@210386e0[variable: featureCounts_biotype]]]
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5bbc9f97[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@133e019b[org.codehaus.groovy.ast.expr.GStringExpression@41382722[strings: [ConstantExpression[], ConstantExpression[_biotype_counts.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@5528a42cnull{ org.codehaus.groovy.ast.stmt.BlockStatement@2a551a63[org.codehaus.groovy.ast.stmt.ExpressionStatement@1a6f5124[expression:org.codehaus.groovy.ast.expr.PropertyExpression@7dac3fd8[object: org.codehaus.groovy.ast.expr.VariableExpression@425357dd[variable: bam_featurecounts] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.641 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@1edb61b1[org.codehaus.groovy.ast.expr.MethodCallExpression@ec2bf82[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[stringtieFPKM] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@cc62a3b[org.codehaus.groovy.ast.expr.ClosureExpression@6cc0bcf6[]{ org.codehaus.groovy.ast.stmt.BlockStatement@29539e36[org.codehaus.groovy.ast.stmt.ExpressionStatement@32f61a31[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f5c79a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@669253b7[org.codehaus.groovy.ast.expr.GStringExpression@5305c37d[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51a06cbe[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddbe65[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@49a64d82[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@344561e0[org.codehaus.groovy.ast.expr.MapExpression@66d23e4a[org.codehaus.groovy.ast.expr.MapEntryExpression@36ac8a63(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@4d9d1b69[strings: [ConstantExpression[], ConstantExpression[/stringtieFPKM]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@52c8295b[object: org.codehaus.groovy.ast.expr.VariableExpression@251f7d26[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@77b21474[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@52d10fb8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41c07648[org.codehaus.groovy.ast.expr.ClosureExpression@1fe8d51b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@781e7326[org.codehaus.groovy.ast.stmt.ExpressionStatement@22680f52[expression:org.codehaus.groovy.ast.expr.BinaryExpression@60d84f61[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@39c11e6c[org.codehaus.groovy.ast.expr.BooleanExpression@324dcd31 ? org.codehaus.groovy.ast.expr.PropertyExpression@503d56b5[object: org.codehaus.groovy.ast.expr.VariableExpression@72bca894[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@433ffad1[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 742:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1fc793c2[object: org.codehaus.groovy.ast.expr.VariableExpression@2575f671[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@329a1243[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@ecf9fb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d35442b[org.codehaus.groovy.ast.expr.ClosureExpression@27f9e982[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4593ff34[org.codehaus.groovy.ast.stmt.ExpressionStatement@37d3d232[expression:org.codehaus.groovy.ast.expr.BinaryExpression@30c0ccff[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@581d969c[org.codehaus.groovy.ast.expr.BooleanExpression@22db8f4 ? org.codehaus.groovy.ast.expr.PropertyExpression@2b46a8c1[object: org.codehaus.groovy.ast.expr.VariableExpression@1d572e62[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@29caf222[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 743:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@46cf05f7[object: org.codehaus.groovy.ast.expr.VariableExpression@5851bd4f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7cd1ac19[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2f40a43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3caa4757[org.codehaus.groovy.ast.expr.VariableExpression@69c43e48[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1804f60d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3a80515c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@547e29a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1c807b1d[org.codehaus.groovy.ast.expr.VariableExpression@238b521e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b39fd82[org.codehaus.groovy.ast.expr.VariableExpression@3e2fc448[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21680803[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@588ab592[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c8b96ec[org.codehaus.groovy.ast.expr.GStringExpression@4cc61eb1[strings: [ConstantExpression[], ConstantExpression[_transcripts.gtf]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d8f2f3a[object: org.codehaus.groovy.ast.expr.VariableExpression@2024293c[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7048f722[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c074c0c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58a55449[org.codehaus.groovy.ast.expr.GStringExpression@5949eba8[strings: [ConstantExpression[], ConstantExpression[.gene_abund.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6e0ff644[object: org.codehaus.groovy.ast.expr.VariableExpression@58dea0a5[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a2bb0eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3c291aad[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d0566ba[org.codehaus.groovy.ast.expr.GStringExpression@733037[strings: [ConstantExpression[], ConstantExpression[.cov_refs.gtf]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7728643a[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@320e400[expression:org.codehaus.groovy.ast.expr.PropertyExpression@5167268[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1cfd1875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[stdout] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@28c0b664[org.codehaus.groovy.ast.expr.VariableExpression@2c444798[variable: into]]] property: ConstantExpression[stringtie_log]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1af7f54a[expression:org.codehaus.groovy.ast.expr.GStringExpression@6ebd78d1[strings: [ConstantExpression[
    stringtie ], ConstantExpression[ \
        -o ], ConstantExpression[_transcripts.gtf \
        -v \
        -G ], ConstantExpression[ \
        -A ], ConstantExpression[.gene_abund.txt \
        -C ], ConstantExpression[.cov_refs.gtf \
        -e \
        -b ], ConstantExpression[_ballgown

    echo "File name: ], ConstantExpression[ Stringtie version "$(stringtie --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@436390f4[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@4d157787[object: org.codehaus.groovy.ast.expr.VariableExpression@68ed96ca[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6d1310f6[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@3228d990[object: org.codehaus.groovy.ast.expr.VariableExpression@54e7391d[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@50b8ae8d[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@255990cc[object: org.codehaus.groovy.ast.expr.VariableExpression@51c929ae[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@3c8bdd5b[variable: bam_stringtieFPKM]]]]] }]]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: stringtieFPKM with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@cc62a3b[org.codehaus.groovy.ast.expr.ClosureExpression@6cc0bcf6[]{ org.codehaus.groovy.ast.stmt.BlockStatement@29539e36[org.codehaus.groovy.ast.stmt.ExpressionStatement@32f61a31[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f5c79a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@669253b7[org.codehaus.groovy.ast.expr.GStringExpression@5305c37d[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51a06cbe[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddbe65[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@49a64d82[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@344561e0[org.codehaus.groovy.ast.expr.MapExpression@66d23e4a[org.codehaus.groovy.ast.expr.MapEntryExpression@36ac8a63(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@4d9d1b69[strings: [ConstantExpression[], ConstantExpression[/stringtieFPKM]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@52c8295b[object: org.codehaus.groovy.ast.expr.VariableExpression@251f7d26[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@77b21474[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@52d10fb8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41c07648[org.codehaus.groovy.ast.expr.ClosureExpression@1fe8d51b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@781e7326[org.codehaus.groovy.ast.stmt.ExpressionStatement@22680f52[expression:org.codehaus.groovy.ast.expr.BinaryExpression@60d84f61[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@39c11e6c[org.codehaus.groovy.ast.expr.BooleanExpression@324dcd31 ? org.codehaus.groovy.ast.expr.PropertyExpression@503d56b5[object: org.codehaus.groovy.ast.expr.VariableExpression@72bca894[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@433ffad1[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 742:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1fc793c2[object: org.codehaus.groovy.ast.expr.VariableExpression@2575f671[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@329a1243[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@ecf9fb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d35442b[org.codehaus.groovy.ast.expr.ClosureExpression@27f9e982[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4593ff34[org.codehaus.groovy.ast.stmt.ExpressionStatement@37d3d232[expression:org.codehaus.groovy.ast.expr.BinaryExpression@30c0ccff[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@581d969c[org.codehaus.groovy.ast.expr.BooleanExpression@22db8f4 ? org.codehaus.groovy.ast.expr.PropertyExpression@2b46a8c1[object: org.codehaus.groovy.ast.expr.VariableExpression@1d572e62[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@29caf222[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 743:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@46cf05f7[object: org.codehaus.groovy.ast.expr.VariableExpression@5851bd4f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7cd1ac19[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2f40a43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3caa4757[org.codehaus.groovy.ast.expr.VariableExpression@69c43e48[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1804f60d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3a80515c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@547e29a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1c807b1d[org.codehaus.groovy.ast.expr.VariableExpression@238b521e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b39fd82[org.codehaus.groovy.ast.expr.VariableExpression@3e2fc448[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21680803[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@588ab592[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c8b96ec[org.codehaus.groovy.ast.expr.GStringExpression@4cc61eb1[strings: [ConstantExpression[], ConstantExpression[_transcripts.gtf]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d8f2f3a[object: org.codehaus.groovy.ast.expr.VariableExpression@2024293c[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7048f722[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c074c0c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58a55449[org.codehaus.groovy.ast.expr.GStringExpression@5949eba8[strings: [ConstantExpression[], ConstantExpression[.gene_abund.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6e0ff644[object: org.codehaus.groovy.ast.expr.VariableExpression@58dea0a5[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a2bb0eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3c291aad[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d0566ba[org.codehaus.groovy.ast.expr.GStringExpression@733037[strings: [ConstantExpression[], ConstantExpression[.cov_refs.gtf]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7728643a[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@320e400[expression:org.codehaus.groovy.ast.expr.PropertyExpression@5167268[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1cfd1875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[stdout] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@28c0b664[org.codehaus.groovy.ast.expr.VariableExpression@2c444798[variable: into]]] property: ConstantExpression[stringtie_log]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1af7f54a[expression:org.codehaus.groovy.ast.expr.GStringExpression@6ebd78d1[strings: [ConstantExpression[
    stringtie ], ConstantExpression[ \
        -o ], ConstantExpression[_transcripts.gtf \
        -v \
        -G ], ConstantExpression[ \
        -A ], ConstantExpression[.gene_abund.txt \
        -C ], ConstantExpression[.cov_refs.gtf \
        -e \
        -b ], ConstantExpression[_ballgown

    echo "File name: ], ConstantExpression[ Stringtie version "$(stringtie --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@436390f4[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@4d157787[object: org.codehaus.groovy.ast.expr.VariableExpression@68ed96ca[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6d1310f6[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@3228d990[object: org.codehaus.groovy.ast.expr.VariableExpression@54e7391d[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@50b8ae8d[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@255990cc[object: org.codehaus.groovy.ast.expr.VariableExpression@51c929ae[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@3c8bdd5b[variable: bam_stringtieFPKM]]]]] }]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@29d2d081[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@cc62a3b[ConstantExpression[stringtieFPKM], org.codehaus.groovy.ast.expr.ClosureExpression@6cc0bcf6[]{ org.codehaus.groovy.ast.stmt.BlockStatement@29539e36[org.codehaus.groovy.ast.stmt.ExpressionStatement@32f61a31[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@f5c79a6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[tag] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@669253b7[org.codehaus.groovy.ast.expr.GStringExpression@5305c37d[strings: [ConstantExpression[], ConstantExpression[]] values: [org.codehaus.groovy.ast.expr.VariableExpression@51a06cbe[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3dddbe65[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@49a64d82[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@344561e0[org.codehaus.groovy.ast.expr.MapExpression@66d23e4a[org.codehaus.groovy.ast.expr.MapEntryExpression@36ac8a63(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@4d9d1b69[strings: [ConstantExpression[], ConstantExpression[/stringtieFPKM]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@52c8295b[object: org.codehaus.groovy.ast.expr.VariableExpression@251f7d26[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@77b21474[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@52d10fb8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@41c07648[org.codehaus.groovy.ast.expr.ClosureExpression@1fe8d51b[]{ org.codehaus.groovy.ast.stmt.BlockStatement@781e7326[org.codehaus.groovy.ast.stmt.ExpressionStatement@22680f52[expression:org.codehaus.groovy.ast.expr.BinaryExpression@60d84f61[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@39c11e6c[org.codehaus.groovy.ast.expr.BooleanExpression@324dcd31 ? org.codehaus.groovy.ast.expr.PropertyExpression@503d56b5[object: org.codehaus.groovy.ast.expr.VariableExpression@72bca894[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@433ffad1[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 742:47:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1fc793c2[object: org.codehaus.groovy.ast.expr.VariableExpression@2575f671[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@329a1243[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@ecf9fb3[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d35442b[org.codehaus.groovy.ast.expr.ClosureExpression@27f9e982[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4593ff34[org.codehaus.groovy.ast.stmt.ExpressionStatement@37d3d232[expression:org.codehaus.groovy.ast.expr.BinaryExpression@30c0ccff[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@581d969c[org.codehaus.groovy.ast.expr.BooleanExpression@22db8f4 ? org.codehaus.groovy.ast.expr.PropertyExpression@2b46a8c1[object: org.codehaus.groovy.ast.expr.VariableExpression@1d572e62[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@29caf222[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 743:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@46cf05f7[object: org.codehaus.groovy.ast.expr.VariableExpression@5851bd4f[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7cd1ac19[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@2f40a43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3caa4757[org.codehaus.groovy.ast.expr.VariableExpression@69c43e48[variable: bam_stringtieFPKM]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1804f60d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3a80515c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@547e29a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1c807b1d[org.codehaus.groovy.ast.expr.VariableExpression@238b521e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b39fd82[org.codehaus.groovy.ast.expr.VariableExpression@3e2fc448[variable: gtf]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@21680803[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@588ab592[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c8b96ec[org.codehaus.groovy.ast.expr.GStringExpression@4cc61eb1[strings: [ConstantExpression[], ConstantExpression[_transcripts.gtf]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@2d8f2f3a[object: org.codehaus.groovy.ast.expr.VariableExpression@2024293c[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7048f722[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@c074c0c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58a55449[org.codehaus.groovy.ast.expr.GStringExpression@5949eba8[strings: [ConstantExpression[], ConstantExpression[.gene_abund.txt]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@6e0ff644[object: org.codehaus.groovy.ast.expr.VariableExpression@58dea0a5[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@2a2bb0eb[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@3c291aad[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d0566ba[org.codehaus.groovy.ast.expr.GStringExpression@733037[strings: [ConstantExpression[], ConstantExpression[.cov_refs.gtf]] values: [org.codehaus.groovy.ast.expr.VariableExpression@7728643a[variable: bam_stringtieFPKM]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@320e400[expression:org.codehaus.groovy.ast.expr.PropertyExpression@5167268[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1cfd1875[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[stdout] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@28c0b664[org.codehaus.groovy.ast.expr.VariableExpression@2c444798[variable: into]]] property: ConstantExpression[stringtie_log]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@1af7f54a[expression:org.codehaus.groovy.ast.expr.GStringExpression@6ebd78d1[strings: [ConstantExpression[
    stringtie ], ConstantExpression[ \
        -o ], ConstantExpression[_transcripts.gtf \
        -v \
        -G ], ConstantExpression[ \
        -A ], ConstantExpression[.gene_abund.txt \
        -C ], ConstantExpression[.cov_refs.gtf \
        -e \
        -b ], ConstantExpression[_ballgown

    echo "File name: ], ConstantExpression[ Stringtie version "$(stringtie --version)
    ]] values: [org.codehaus.groovy.ast.expr.VariableExpression@436390f4[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@4d157787[object: org.codehaus.groovy.ast.expr.VariableExpression@68ed96ca[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@6d1310f6[variable: gtf], org.codehaus.groovy.ast.expr.PropertyExpression@3228d990[object: org.codehaus.groovy.ast.expr.VariableExpression@54e7391d[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@50b8ae8d[variable: bam_stringtieFPKM], org.codehaus.groovy.ast.expr.PropertyExpression@255990cc[object: org.codehaus.groovy.ast.expr.VariableExpression@51c929ae[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]], org.codehaus.groovy.ast.expr.VariableExpression@3c8bdd5b[variable: bam_stringtieFPKM]]]]] }]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@2f40a43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3caa4757[org.codehaus.groovy.ast.expr.VariableExpression@69c43e48[variable: bam_stringtieFPKM]]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3a80515c[object: org.codehaus.groovy.ast.expr.MethodCallExpression@547e29a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1c807b1d[org.codehaus.groovy.ast.expr.VariableExpression@238b521e[variable: gtf]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1b39fd82[org.codehaus.groovy.ast.expr.VariableExpression@3e2fc448[variable: gtf]]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@547e29a4[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1c807b1d[org.codehaus.groovy.ast.expr.VariableExpression@238b521e[variable: gtf]]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@588ab592[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@c8b96ec[org.codehaus.groovy.ast.expr.GStringExpression@4cc61eb1[strings: [ConstantExpression[], ConstantExpression[_transcripts.gtf]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@40e4ea87null{ org.codehaus.groovy.ast.stmt.BlockStatement@58783f6c[org.codehaus.groovy.ast.stmt.ExpressionStatement@3a7b503d[expression:org.codehaus.groovy.ast.expr.PropertyExpression@2d8f2f3a[object: org.codehaus.groovy.ast.expr.VariableExpression@2024293c[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.643 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@c074c0c[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58a55449[org.codehaus.groovy.ast.expr.GStringExpression@5949eba8[strings: [ConstantExpression[], ConstantExpression[.gene_abund.txt]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@512d92bnull{ org.codehaus.groovy.ast.stmt.BlockStatement@62c5bbdc[org.codehaus.groovy.ast.stmt.ExpressionStatement@7bdf6bb7[expression:org.codehaus.groovy.ast.expr.PropertyExpression@6e0ff644[object: org.codehaus.groovy.ast.expr.VariableExpression@58dea0a5[variable: bam_stringtieFPKM] property: ConstantExpression[baseName]]]] }]]]]
Nov-14 16:09:26.644 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.644 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3c291aad[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2d0566ba[org.codehaus.groovy.ast.expr.GStringExpression@733037[strings: [ConstantExpression[], ConstantExpression[.cov_refs.gtf]] values: [org.codehaus.groovy.ast.expr.ClosureExpression@1bc53649null{ org.codehaus.groovy.ast.stmt.BlockStatement@88d6f9b[org.codehaus.groovy.ast.stmt.ExpressionStatement@47d93e0d[expression:org.codehaus.groovy.ast.expr.VariableExpression@7728643a[variable: bam_stringtieFPKM]]] }]]]]
Nov-14 16:09:26.644 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.645 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@751e664e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@160c3ec1[object: org.codehaus.groovy.ast.expr.VariableExpression@182b435b[variable: this] method: ConstantExpression[stdout] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4d0402b[]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fa7ae9[org.codehaus.groovy.ast.expr.VariableExpression@7577b641[variable: stringtie_log]]]
Nov-14 16:09:26.645 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.645 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@160c3ec1[object: org.codehaus.groovy.ast.expr.VariableExpression@182b435b[variable: this] method: ConstantExpression[stdout] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4d0402b[]]
Nov-14 16:09:26.645 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: stdout
Nov-14 16:09:26.646 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@60afd40d[org.codehaus.groovy.ast.expr.MethodCallExpression@28a2a3e7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[sample_correlation] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f2049b6[org.codehaus.groovy.ast.expr.ClosureExpression@10b3df93[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ea27e34[org.codehaus.groovy.ast.stmt.ExpressionStatement@33a2499c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e72dba7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@33c2bd[org.codehaus.groovy.ast.expr.MapExpression@1dfd5f51[org.codehaus.groovy.ast.expr.MapEntryExpression@3c321bdb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@24855019[strings: [ConstantExpression[], ConstantExpression[/sample_correlation]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3abd581e[object: org.codehaus.groovy.ast.expr.VariableExpression@4d4d8fcf[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@610db97e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f0628de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fabf088[org.codehaus.groovy.ast.expr.ClosureExpression@1e392345[]{ org.codehaus.groovy.ast.stmt.BlockStatement@12f3afb5[org.codehaus.groovy.ast.stmt.ExpressionStatement@4ced35ed[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2c22a348[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7bd69e82[org.codehaus.groovy.ast.expr.BooleanExpression@74d7184a ? org.codehaus.groovy.ast.expr.PropertyExpression@51b01960[object: org.codehaus.groovy.ast.expr.VariableExpression@6831d8fd[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@27dc79f7[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 780:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6b85300e[object: org.codehaus.groovy.ast.expr.VariableExpression@3aaf4f07[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5cbf9e9f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@18e8473e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a2f016d[org.codehaus.groovy.ast.expr.ClosureExpression@1a38ba58[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ad394e6[org.codehaus.groovy.ast.stmt.ExpressionStatement@6058e535[expression:org.codehaus.groovy.ast.expr.BinaryExpression@42deb43a[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1deb2c43[org.codehaus.groovy.ast.expr.BooleanExpression@3bb9efbc ? org.codehaus.groovy.ast.expr.PropertyExpression@1cefc4b3[object: org.codehaus.groovy.ast.expr.VariableExpression@2b27cc70[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6f6a7463[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 781:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1bdaa23d[object: org.codehaus.groovy.ast.expr.VariableExpression@79f227a9[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6ca320ab[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50d68830[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e53135d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7674a051[org.codehaus.groovy.ast.expr.VariableExpression@3a7704c[variable: input_files]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6754ef00[org.codehaus.groovy.ast.expr.MethodCallExpression@619bd14c[object: org.codehaus.groovy.ast.expr.VariableExpression@323e8306[variable: geneCounts] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a23a01d[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4acf72b6[expression:org.codehaus.groovy.ast.expr.VariableExpression@7561db12[variable: bam_count]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3301500b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@24b52d3e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@15deb1dc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e9c413e[ConstantExpression[*.{txt,pdf}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57a4d5ee[org.codehaus.groovy.ast.expr.VariableExpression@5af5def9[variable: sample_correlation_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a45c42a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@36dce7ed[org.codehaus.groovy.ast.expr.BinaryExpression@47a64f7d[org.codehaus.groovy.ast.expr.VariableExpression@33d05366[variable: num_bams](">" at 791:14:  ">" )ConstantExpression[2]]("&&" at 791:18:  "&&" )org.codehaus.groovy.ast.expr.NotExpression@27a0a5a2]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7692cd34[expression:org.codehaus.groovy.ast.expr.GStringExpression@33aa93c[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install required packages
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("limma")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("limma", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("limma")
    }

    if (!require("edgeR")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("edgeR", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("edgeR")
    }

    if (!require("data.table")){
        install.packages("data.table", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("data.table")
    }

    if (!require("gplots")) {
        install.packages("gplots", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("gplots")
    }

    # Load input counts data
    datafiles = c( "], ConstantExpression[" )

    # Load count column from all files into a list of data frames
    # Use data.tables fread as much much faster than read.table
    # Row names are GeneIDs
    temp <- lapply(datafiles, fread, skip="Geneid", header=TRUE, colClasses=c(NA, rep("NULL", 5), NA))

    # Merge into a single data frame
    merge.all <- function(x, y) {
        merge(x, y, all=TRUE, by="Geneid")
    }
    data <- data.frame(Reduce(merge.all, temp))

    # Clean sample name headers
    colnames(data) <- gsub("Aligned.sortedByCoord.out.bam", "", colnames(data))

    # Set GeneID as row name
    rownames(data) <- data[,1]
    data[,1] <- NULL

    # Convert data frame to edgeR DGE object
    dataDGE <- DGEList( counts=data.matrix(data) )

    # Normalise counts
    dataNorm <- calcNormFactors(dataDGE)

    # Make MDS plot
    pdf('edgeR_MDS_plot.pdf')
    MDSdata <- plotMDS(dataNorm)
    dev.off()

    # Print distance matrix to file
    write.table(MDSdata$distance.matrix, 'edgeR_MDS_distance_matrix.txt', quote=FALSE, sep="\t")

    # Print plot x,y co-ordinates to file
    MDSxy = MDSdata$cmdscale.out
    colnames(MDSxy) = c(paste(MDSdata$axislabel, '1'), paste(MDSdata$axislabel, '2'))
    write.table(MDSxy, 'edgeR_MDS_plot_coordinates.txt', quote=FALSE, sep="\t")

    # Get the log counts per million values
    logcpm <- cpm(dataNorm, prior.count=2, log=TRUE)

    # Calculate the euclidean distances between samples
    dists = dist(t(logcpm))

    # Plot a heatmap of correlations
    pdf('log2CPM_sample_distances_heatmap.pdf')
    hmap <- heatmap.2(as.matrix(dists),
      main="Sample Correlations", key.title="Distance", trace="none",
      dendrogram="row", margin=c(9, 9)
    )
    dev.off()

    # Plot the heatmap dendrogram
    pdf('log2CPM_sample_distances_dendrogram.pdf')
    plot(hmap$rowDendrogram, main="Sample Dendrogram")
    dev.off()

    # Write clustered distance values to file
    write.table(hmap$carpet, 'log2CPM_sample_distances.txt', quote=FALSE, sep="\t")

    file.create("corr.done")

    # Printing sessioninfo to standard out
    print("Sample correlation info:")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@32c0915e[object: org.codehaus.groovy.ast.expr.VariableExpression@106faf11[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@70f43b45[object: org.codehaus.groovy.ast.expr.VariableExpression@26d10f2e[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@10ad20cb[object: org.codehaus.groovy.ast.expr.VariableExpression@7dd712e8[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@2c282004[object: org.codehaus.groovy.ast.expr.VariableExpression@22ee2d0[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@7bfc3126[object: org.codehaus.groovy.ast.expr.VariableExpression@3e792ce3[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.MethodCallExpression@53bc1328[object: org.codehaus.groovy.ast.expr.CastExpression@26f143ed[(List) org.codehaus.groovy.ast.expr.VariableExpression@3c1e3314[variable: input_files]] method: ConstantExpression[join] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b770e40[ConstantExpression[", "]]]]]]] }]]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: sample_correlation with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f2049b6[org.codehaus.groovy.ast.expr.ClosureExpression@10b3df93[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ea27e34[org.codehaus.groovy.ast.stmt.ExpressionStatement@33a2499c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e72dba7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@33c2bd[org.codehaus.groovy.ast.expr.MapExpression@1dfd5f51[org.codehaus.groovy.ast.expr.MapEntryExpression@3c321bdb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@24855019[strings: [ConstantExpression[], ConstantExpression[/sample_correlation]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3abd581e[object: org.codehaus.groovy.ast.expr.VariableExpression@4d4d8fcf[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@610db97e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f0628de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fabf088[org.codehaus.groovy.ast.expr.ClosureExpression@1e392345[]{ org.codehaus.groovy.ast.stmt.BlockStatement@12f3afb5[org.codehaus.groovy.ast.stmt.ExpressionStatement@4ced35ed[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2c22a348[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7bd69e82[org.codehaus.groovy.ast.expr.BooleanExpression@74d7184a ? org.codehaus.groovy.ast.expr.PropertyExpression@51b01960[object: org.codehaus.groovy.ast.expr.VariableExpression@6831d8fd[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@27dc79f7[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 780:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6b85300e[object: org.codehaus.groovy.ast.expr.VariableExpression@3aaf4f07[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5cbf9e9f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@18e8473e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a2f016d[org.codehaus.groovy.ast.expr.ClosureExpression@1a38ba58[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ad394e6[org.codehaus.groovy.ast.stmt.ExpressionStatement@6058e535[expression:org.codehaus.groovy.ast.expr.BinaryExpression@42deb43a[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1deb2c43[org.codehaus.groovy.ast.expr.BooleanExpression@3bb9efbc ? org.codehaus.groovy.ast.expr.PropertyExpression@1cefc4b3[object: org.codehaus.groovy.ast.expr.VariableExpression@2b27cc70[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6f6a7463[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 781:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1bdaa23d[object: org.codehaus.groovy.ast.expr.VariableExpression@79f227a9[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6ca320ab[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50d68830[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e53135d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7674a051[org.codehaus.groovy.ast.expr.VariableExpression@3a7704c[variable: input_files]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6754ef00[org.codehaus.groovy.ast.expr.MethodCallExpression@619bd14c[object: org.codehaus.groovy.ast.expr.VariableExpression@323e8306[variable: geneCounts] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a23a01d[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4acf72b6[expression:org.codehaus.groovy.ast.expr.VariableExpression@7561db12[variable: bam_count]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3301500b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@24b52d3e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@15deb1dc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e9c413e[ConstantExpression[*.{txt,pdf}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57a4d5ee[org.codehaus.groovy.ast.expr.VariableExpression@5af5def9[variable: sample_correlation_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a45c42a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@36dce7ed[org.codehaus.groovy.ast.expr.BinaryExpression@47a64f7d[org.codehaus.groovy.ast.expr.VariableExpression@33d05366[variable: num_bams](">" at 791:14:  ">" )ConstantExpression[2]]("&&" at 791:18:  "&&" )org.codehaus.groovy.ast.expr.NotExpression@27a0a5a2]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7692cd34[expression:org.codehaus.groovy.ast.expr.GStringExpression@33aa93c[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install required packages
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("limma")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("limma", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("limma")
    }

    if (!require("edgeR")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("edgeR", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("edgeR")
    }

    if (!require("data.table")){
        install.packages("data.table", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("data.table")
    }

    if (!require("gplots")) {
        install.packages("gplots", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("gplots")
    }

    # Load input counts data
    datafiles = c( "], ConstantExpression[" )

    # Load count column from all files into a list of data frames
    # Use data.tables fread as much much faster than read.table
    # Row names are GeneIDs
    temp <- lapply(datafiles, fread, skip="Geneid", header=TRUE, colClasses=c(NA, rep("NULL", 5), NA))

    # Merge into a single data frame
    merge.all <- function(x, y) {
        merge(x, y, all=TRUE, by="Geneid")
    }
    data <- data.frame(Reduce(merge.all, temp))

    # Clean sample name headers
    colnames(data) <- gsub("Aligned.sortedByCoord.out.bam", "", colnames(data))

    # Set GeneID as row name
    rownames(data) <- data[,1]
    data[,1] <- NULL

    # Convert data frame to edgeR DGE object
    dataDGE <- DGEList( counts=data.matrix(data) )

    # Normalise counts
    dataNorm <- calcNormFactors(dataDGE)

    # Make MDS plot
    pdf('edgeR_MDS_plot.pdf')
    MDSdata <- plotMDS(dataNorm)
    dev.off()

    # Print distance matrix to file
    write.table(MDSdata$distance.matrix, 'edgeR_MDS_distance_matrix.txt', quote=FALSE, sep="\t")

    # Print plot x,y co-ordinates to file
    MDSxy = MDSdata$cmdscale.out
    colnames(MDSxy) = c(paste(MDSdata$axislabel, '1'), paste(MDSdata$axislabel, '2'))
    write.table(MDSxy, 'edgeR_MDS_plot_coordinates.txt', quote=FALSE, sep="\t")

    # Get the log counts per million values
    logcpm <- cpm(dataNorm, prior.count=2, log=TRUE)

    # Calculate the euclidean distances between samples
    dists = dist(t(logcpm))

    # Plot a heatmap of correlations
    pdf('log2CPM_sample_distances_heatmap.pdf')
    hmap <- heatmap.2(as.matrix(dists),
      main="Sample Correlations", key.title="Distance", trace="none",
      dendrogram="row", margin=c(9, 9)
    )
    dev.off()

    # Plot the heatmap dendrogram
    pdf('log2CPM_sample_distances_dendrogram.pdf')
    plot(hmap$rowDendrogram, main="Sample Dendrogram")
    dev.off()

    # Write clustered distance values to file
    write.table(hmap$carpet, 'log2CPM_sample_distances.txt', quote=FALSE, sep="\t")

    file.create("corr.done")

    # Printing sessioninfo to standard out
    print("Sample correlation info:")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@32c0915e[object: org.codehaus.groovy.ast.expr.VariableExpression@106faf11[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@70f43b45[object: org.codehaus.groovy.ast.expr.VariableExpression@26d10f2e[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@10ad20cb[object: org.codehaus.groovy.ast.expr.VariableExpression@7dd712e8[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@2c282004[object: org.codehaus.groovy.ast.expr.VariableExpression@22ee2d0[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@7bfc3126[object: org.codehaus.groovy.ast.expr.VariableExpression@3e792ce3[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.MethodCallExpression@53bc1328[object: org.codehaus.groovy.ast.expr.CastExpression@26f143ed[(List) org.codehaus.groovy.ast.expr.VariableExpression@3c1e3314[variable: input_files]] method: ConstantExpression[join] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b770e40[ConstantExpression[", "]]]]]]] }]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@78e16155[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f2049b6[ConstantExpression[sample_correlation], org.codehaus.groovy.ast.expr.ClosureExpression@10b3df93[]{ org.codehaus.groovy.ast.stmt.BlockStatement@ea27e34[org.codehaus.groovy.ast.stmt.ExpressionStatement@33a2499c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e72dba7[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@33c2bd[org.codehaus.groovy.ast.expr.MapExpression@1dfd5f51[org.codehaus.groovy.ast.expr.MapEntryExpression@3c321bdb(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@24855019[strings: [ConstantExpression[], ConstantExpression[/sample_correlation]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3abd581e[object: org.codehaus.groovy.ast.expr.VariableExpression@4d4d8fcf[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@610db97e[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6f0628de[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fabf088[org.codehaus.groovy.ast.expr.ClosureExpression@1e392345[]{ org.codehaus.groovy.ast.stmt.BlockStatement@12f3afb5[org.codehaus.groovy.ast.stmt.ExpressionStatement@4ced35ed[expression:org.codehaus.groovy.ast.expr.BinaryExpression@2c22a348[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@7bd69e82[org.codehaus.groovy.ast.expr.BooleanExpression@74d7184a ? org.codehaus.groovy.ast.expr.PropertyExpression@51b01960[object: org.codehaus.groovy.ast.expr.VariableExpression@6831d8fd[variable: params] property: ConstantExpression[dupradar_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@27dc79f7[object: ConstantExpression[16] property: ConstantExpression[GB]]]("*" at 780:48:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@6b85300e[object: org.codehaus.groovy.ast.expr.VariableExpression@3aaf4f07[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5cbf9e9f[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@18e8473e[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a2f016d[org.codehaus.groovy.ast.expr.ClosureExpression@1a38ba58[]{ org.codehaus.groovy.ast.stmt.BlockStatement@3ad394e6[org.codehaus.groovy.ast.stmt.ExpressionStatement@6058e535[expression:org.codehaus.groovy.ast.expr.BinaryExpression@42deb43a[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@1deb2c43[org.codehaus.groovy.ast.expr.BooleanExpression@3bb9efbc ? org.codehaus.groovy.ast.expr.PropertyExpression@1cefc4b3[object: org.codehaus.groovy.ast.expr.VariableExpression@2b27cc70[variable: params] property: ConstantExpression[dupradar_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@6f6a7463[object: ConstantExpression[2] property: ConstantExpression[h]]]("*" at 781:42:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@1bdaa23d[object: org.codehaus.groovy.ast.expr.VariableExpression@79f227a9[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6ca320ab[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50d68830[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e53135d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7674a051[org.codehaus.groovy.ast.expr.VariableExpression@3a7704c[variable: input_files]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6754ef00[org.codehaus.groovy.ast.expr.MethodCallExpression@619bd14c[object: org.codehaus.groovy.ast.expr.VariableExpression@323e8306[variable: geneCounts] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a23a01d[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@4acf72b6[expression:org.codehaus.groovy.ast.expr.VariableExpression@7561db12[variable: bam_count]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3301500b[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@24b52d3e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@15deb1dc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e9c413e[ConstantExpression[*.{txt,pdf}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57a4d5ee[org.codehaus.groovy.ast.expr.VariableExpression@5af5def9[variable: sample_correlation_results]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3a45c42a[expression:org.codehaus.groovy.ast.expr.BinaryExpression@36dce7ed[org.codehaus.groovy.ast.expr.BinaryExpression@47a64f7d[org.codehaus.groovy.ast.expr.VariableExpression@33d05366[variable: num_bams](">" at 791:14:  ">" )ConstantExpression[2]]("&&" at 791:18:  "&&" )org.codehaus.groovy.ast.expr.NotExpression@27a0a5a2]], org.codehaus.groovy.ast.stmt.ExpressionStatement@7692cd34[expression:org.codehaus.groovy.ast.expr.GStringExpression@33aa93c[strings: [ConstantExpression[
    #!/usr/bin/env Rscript

    # Load / install required packages
    .libPaths( c( "], ConstantExpression[", .libPaths() ) )
    if (!require("limma")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("limma", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("limma")
    }

    if (!require("edgeR")){
        source("http://bioconductor.org/biocLite.R")
        biocLite("edgeR", suppressUpdates=TRUE, lib="], ConstantExpression[")
        library("edgeR")
    }

    if (!require("data.table")){
        install.packages("data.table", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("data.table")
    }

    if (!require("gplots")) {
        install.packages("gplots", dependencies=TRUE, repos='http://cloud.r-project.org/', lib="], ConstantExpression[")
        library("gplots")
    }

    # Load input counts data
    datafiles = c( "], ConstantExpression[" )

    # Load count column from all files into a list of data frames
    # Use data.tables fread as much much faster than read.table
    # Row names are GeneIDs
    temp <- lapply(datafiles, fread, skip="Geneid", header=TRUE, colClasses=c(NA, rep("NULL", 5), NA))

    # Merge into a single data frame
    merge.all <- function(x, y) {
        merge(x, y, all=TRUE, by="Geneid")
    }
    data <- data.frame(Reduce(merge.all, temp))

    # Clean sample name headers
    colnames(data) <- gsub("Aligned.sortedByCoord.out.bam", "", colnames(data))

    # Set GeneID as row name
    rownames(data) <- data[,1]
    data[,1] <- NULL

    # Convert data frame to edgeR DGE object
    dataDGE <- DGEList( counts=data.matrix(data) )

    # Normalise counts
    dataNorm <- calcNormFactors(dataDGE)

    # Make MDS plot
    pdf('edgeR_MDS_plot.pdf')
    MDSdata <- plotMDS(dataNorm)
    dev.off()

    # Print distance matrix to file
    write.table(MDSdata$distance.matrix, 'edgeR_MDS_distance_matrix.txt', quote=FALSE, sep="\t")

    # Print plot x,y co-ordinates to file
    MDSxy = MDSdata$cmdscale.out
    colnames(MDSxy) = c(paste(MDSdata$axislabel, '1'), paste(MDSdata$axislabel, '2'))
    write.table(MDSxy, 'edgeR_MDS_plot_coordinates.txt', quote=FALSE, sep="\t")

    # Get the log counts per million values
    logcpm <- cpm(dataNorm, prior.count=2, log=TRUE)

    # Calculate the euclidean distances between samples
    dists = dist(t(logcpm))

    # Plot a heatmap of correlations
    pdf('log2CPM_sample_distances_heatmap.pdf')
    hmap <- heatmap.2(as.matrix(dists),
      main="Sample Correlations", key.title="Distance", trace="none",
      dendrogram="row", margin=c(9, 9)
    )
    dev.off()

    # Plot the heatmap dendrogram
    pdf('log2CPM_sample_distances_dendrogram.pdf')
    plot(hmap$rowDendrogram, main="Sample Dendrogram")
    dev.off()

    # Write clustered distance values to file
    write.table(hmap$carpet, 'log2CPM_sample_distances.txt', quote=FALSE, sep="\t")

    file.create("corr.done")

    # Printing sessioninfo to standard out
    print("Sample correlation info:")
    sessionInfo()
    ]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@32c0915e[object: org.codehaus.groovy.ast.expr.VariableExpression@106faf11[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@70f43b45[object: org.codehaus.groovy.ast.expr.VariableExpression@26d10f2e[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@10ad20cb[object: org.codehaus.groovy.ast.expr.VariableExpression@7dd712e8[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@2c282004[object: org.codehaus.groovy.ast.expr.VariableExpression@22ee2d0[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.PropertyExpression@7bfc3126[object: org.codehaus.groovy.ast.expr.VariableExpression@3e792ce3[variable: params] property: ConstantExpression[rlocation]], org.codehaus.groovy.ast.expr.MethodCallExpression@53bc1328[object: org.codehaus.groovy.ast.expr.CastExpression@26f143ed[(List) org.codehaus.groovy.ast.expr.VariableExpression@3c1e3314[variable: input_files]] method: ConstantExpression[join] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@4b770e40[ConstantExpression[", "]]]]]]] }]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@50d68830[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1e53135d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7674a051[org.codehaus.groovy.ast.expr.VariableExpression@3a7704c[variable: input_files]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6754ef00[org.codehaus.groovy.ast.expr.MethodCallExpression@619bd14c[object: org.codehaus.groovy.ast.expr.VariableExpression@323e8306[variable: geneCounts] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@a23a01d[]]]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1e53135d[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7674a051[org.codehaus.groovy.ast.expr.VariableExpression@3a7704c[variable: input_files]]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.VariableExpression@7561db12[variable: bam_count]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@24b52d3e[object: org.codehaus.groovy.ast.expr.MethodCallExpression@15deb1dc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e9c413e[ConstantExpression[*.{txt,pdf}]]] method: ConstantExpression[into] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57a4d5ee[org.codehaus.groovy.ast.expr.VariableExpression@5af5def9[variable: sample_correlation_results]]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: into
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@15deb1dc[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6e9c413e[ConstantExpression[*.{txt,pdf}]]]
Nov-14 16:09:26.647 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.653 [main] TRACE nextflow.ast.NextflowDSLImpl - Converts 'process' org.codehaus.groovy.ast.expr.ArgumentListExpression@6a1ebcff[org.codehaus.groovy.ast.expr.MethodCallExpression@19868320[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[multiqc] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@50b0bc4c[org.codehaus.groovy.ast.expr.ClosureExpression@c20be82[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13c612bd[org.codehaus.groovy.ast.stmt.ExpressionStatement@3ef41c66[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6b739528[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@622ef26a[org.codehaus.groovy.ast.expr.MapExpression@41de5768[org.codehaus.groovy.ast.expr.MapEntryExpression@5f577419(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@28fa700e[strings: [ConstantExpression[], ConstantExpression[/MultiQC]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3d526ad9[object: org.codehaus.groovy.ast.expr.VariableExpression@e041f0c[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a175569[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11963225[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f3c966c[org.codehaus.groovy.ast.expr.ClosureExpression@11ee02f8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4102b1b1[org.codehaus.groovy.ast.stmt.ExpressionStatement@61a5b4ae[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3a71c100[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@5b69fd74[org.codehaus.groovy.ast.expr.BooleanExpression@f325091 ? org.codehaus.groovy.ast.expr.PropertyExpression@437e951d[object: org.codehaus.groovy.ast.expr.VariableExpression@77b325b3[variable: params] property: ConstantExpression[multiqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@63a5e46c[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 898:46:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7e8e8651[object: org.codehaus.groovy.ast.expr.VariableExpression@49ef32e0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@271f18d3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6bd51ed8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@61e3a1fd[org.codehaus.groovy.ast.expr.ClosureExpression@51abf713[]{ org.codehaus.groovy.ast.stmt.BlockStatement@eadb475[org.codehaus.groovy.ast.stmt.ExpressionStatement@4d4d48a6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@315df4bb[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fc08eec[org.codehaus.groovy.ast.expr.BooleanExpression@5cad8b7d ? org.codehaus.groovy.ast.expr.PropertyExpression@7b02e036[object: org.codehaus.groovy.ast.expr.VariableExpression@25243bc1[variable: params] property: ConstantExpression[multiqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1e287667[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 899:41:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2e6ee0bc[object: org.codehaus.groovy.ast.expr.VariableExpression@4201a617[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@467f77a5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1bb9aa43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@420bc288[ConstantExpression[ignore]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@df5f5c0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@308a6984[object: org.codehaus.groovy.ast.expr.MethodCallExpression@66b72664[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a34b7b8[ConstantExpression[fastqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58cd06cb[org.codehaus.groovy.ast.expr.MethodCallExpression@3be8821f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@64b31700[object: org.codehaus.groovy.ast.expr.VariableExpression@3b65e559[variable: fastqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@bae47a0[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@74a9c4b0[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@85ec632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c05a54d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@65ef722a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5fd9b663[ConstantExpression[trimgalore/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@214894fc[org.codehaus.groovy.ast.expr.MethodCallExpression@10567255[object: org.codehaus.groovy.ast.expr.MethodCallExpression@e362c57[object: org.codehaus.groovy.ast.expr.VariableExpression@1c4ee95c[variable: trimgalore_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@79c4715d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5aa360ea[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6548bb7d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e27ba81[object: org.codehaus.groovy.ast.expr.MethodCallExpression@54336c81[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1556f2dd[ConstantExpression[alignment/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@35e52059[org.codehaus.groovy.ast.expr.MethodCallExpression@62577d6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bd54f7[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5f8707[variable: alignment_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@772485dd[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a12c728[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79ab3a71[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e5bfdfc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d829787[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71652c98[ConstantExpression[rseqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51bde877[org.codehaus.groovy.ast.expr.MethodCallExpression@60b85ba1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@492fc69e[object: org.codehaus.groovy.ast.expr.VariableExpression@117632cf[variable: rseqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fb68ec6[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d71adc2[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3add81c4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1a1d3c1a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1c65121[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@159e366[ConstantExpression[preseq/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57dc9128[org.codehaus.groovy.ast.expr.MethodCallExpression@24528a25[object: org.codehaus.groovy.ast.expr.MethodCallExpression@17ae98d7[object: org.codehaus.groovy.ast.expr.VariableExpression@59221b97[variable: preseq_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ac4944a[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a772895[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@39fc6b2c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@704b2127[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3ee39da0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d332969[ConstantExpression[dupradar/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cc9ce8[org.codehaus.groovy.ast.expr.MethodCallExpression@2e27d72f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@c0b41d6[object: org.codehaus.groovy.ast.expr.VariableExpression@4837595f[variable: dupradar_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2bffa76d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b718392[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6d2260db[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1f2d2181[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bf29c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7ee55e70[ConstantExpression[featureCounts/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fcdcf[org.codehaus.groovy.ast.expr.MethodCallExpression@7668d560[object: org.codehaus.groovy.ast.expr.MethodCallExpression@46292372[object: org.codehaus.groovy.ast.expr.VariableExpression@126be319[variable: featureCounts_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c44052e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c371e13[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@530a8454[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e34c607[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5215cd9a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b6964d[ConstantExpression[featureCounts_biotype/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31198ceb[org.codehaus.groovy.ast.expr.MethodCallExpression@9257031[object: org.codehaus.groovy.ast.expr.MethodCallExpression@75201592[object: org.codehaus.groovy.ast.expr.VariableExpression@7726e185[variable: featureCounts_biotype] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@aa5455e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@282308c3[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5dda14d0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1db0ec27[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d9fc57a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d4ab71a[ConstantExpression[stringtie/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b4ef7[org.codehaus.groovy.ast.expr.MethodCallExpression@1af05b03[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5987e932[object: org.codehaus.groovy.ast.expr.VariableExpression@1ad777f[variable: stringtie_log] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bbbdd4b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@438bad7c[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25230246[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fdf8f12[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a8b5227[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@54f5f647[ConstantExpression[sample_correlation_results/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6979efad[org.codehaus.groovy.ast.expr.MethodCallExpression@5a6d5a8f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a67318f[object: org.codehaus.groovy.ast.expr.VariableExpression@315ba14a[variable: sample_correlation_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@17f9344b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27f0ad19[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54e81b21[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@38d5b107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6650813a[ConstantExpression[*multiqc_report.html]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@44ea608c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50cf5a23[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@450794b4[ConstantExpression[*multiqc_data]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@273c947f[expression:ConstantExpression[
    multiqc -f .
    ]]] }]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - Process name: multiqc with args: org.codehaus.groovy.ast.expr.ArgumentListExpression@50b0bc4c[org.codehaus.groovy.ast.expr.ClosureExpression@c20be82[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13c612bd[org.codehaus.groovy.ast.stmt.ExpressionStatement@3ef41c66[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6b739528[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@622ef26a[org.codehaus.groovy.ast.expr.MapExpression@41de5768[org.codehaus.groovy.ast.expr.MapEntryExpression@5f577419(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@28fa700e[strings: [ConstantExpression[], ConstantExpression[/MultiQC]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3d526ad9[object: org.codehaus.groovy.ast.expr.VariableExpression@e041f0c[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a175569[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11963225[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f3c966c[org.codehaus.groovy.ast.expr.ClosureExpression@11ee02f8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4102b1b1[org.codehaus.groovy.ast.stmt.ExpressionStatement@61a5b4ae[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3a71c100[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@5b69fd74[org.codehaus.groovy.ast.expr.BooleanExpression@f325091 ? org.codehaus.groovy.ast.expr.PropertyExpression@437e951d[object: org.codehaus.groovy.ast.expr.VariableExpression@77b325b3[variable: params] property: ConstantExpression[multiqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@63a5e46c[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 898:46:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7e8e8651[object: org.codehaus.groovy.ast.expr.VariableExpression@49ef32e0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@271f18d3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6bd51ed8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@61e3a1fd[org.codehaus.groovy.ast.expr.ClosureExpression@51abf713[]{ org.codehaus.groovy.ast.stmt.BlockStatement@eadb475[org.codehaus.groovy.ast.stmt.ExpressionStatement@4d4d48a6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@315df4bb[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fc08eec[org.codehaus.groovy.ast.expr.BooleanExpression@5cad8b7d ? org.codehaus.groovy.ast.expr.PropertyExpression@7b02e036[object: org.codehaus.groovy.ast.expr.VariableExpression@25243bc1[variable: params] property: ConstantExpression[multiqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1e287667[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 899:41:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2e6ee0bc[object: org.codehaus.groovy.ast.expr.VariableExpression@4201a617[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@467f77a5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1bb9aa43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@420bc288[ConstantExpression[ignore]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@df5f5c0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@308a6984[object: org.codehaus.groovy.ast.expr.MethodCallExpression@66b72664[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a34b7b8[ConstantExpression[fastqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58cd06cb[org.codehaus.groovy.ast.expr.MethodCallExpression@3be8821f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@64b31700[object: org.codehaus.groovy.ast.expr.VariableExpression@3b65e559[variable: fastqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@bae47a0[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@74a9c4b0[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@85ec632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c05a54d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@65ef722a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5fd9b663[ConstantExpression[trimgalore/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@214894fc[org.codehaus.groovy.ast.expr.MethodCallExpression@10567255[object: org.codehaus.groovy.ast.expr.MethodCallExpression@e362c57[object: org.codehaus.groovy.ast.expr.VariableExpression@1c4ee95c[variable: trimgalore_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@79c4715d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5aa360ea[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6548bb7d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e27ba81[object: org.codehaus.groovy.ast.expr.MethodCallExpression@54336c81[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1556f2dd[ConstantExpression[alignment/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@35e52059[org.codehaus.groovy.ast.expr.MethodCallExpression@62577d6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bd54f7[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5f8707[variable: alignment_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@772485dd[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a12c728[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79ab3a71[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e5bfdfc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d829787[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71652c98[ConstantExpression[rseqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51bde877[org.codehaus.groovy.ast.expr.MethodCallExpression@60b85ba1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@492fc69e[object: org.codehaus.groovy.ast.expr.VariableExpression@117632cf[variable: rseqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fb68ec6[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d71adc2[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3add81c4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1a1d3c1a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1c65121[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@159e366[ConstantExpression[preseq/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57dc9128[org.codehaus.groovy.ast.expr.MethodCallExpression@24528a25[object: org.codehaus.groovy.ast.expr.MethodCallExpression@17ae98d7[object: org.codehaus.groovy.ast.expr.VariableExpression@59221b97[variable: preseq_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ac4944a[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a772895[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@39fc6b2c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@704b2127[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3ee39da0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d332969[ConstantExpression[dupradar/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cc9ce8[org.codehaus.groovy.ast.expr.MethodCallExpression@2e27d72f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@c0b41d6[object: org.codehaus.groovy.ast.expr.VariableExpression@4837595f[variable: dupradar_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2bffa76d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b718392[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6d2260db[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1f2d2181[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bf29c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7ee55e70[ConstantExpression[featureCounts/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fcdcf[org.codehaus.groovy.ast.expr.MethodCallExpression@7668d560[object: org.codehaus.groovy.ast.expr.MethodCallExpression@46292372[object: org.codehaus.groovy.ast.expr.VariableExpression@126be319[variable: featureCounts_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c44052e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c371e13[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@530a8454[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e34c607[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5215cd9a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b6964d[ConstantExpression[featureCounts_biotype/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31198ceb[org.codehaus.groovy.ast.expr.MethodCallExpression@9257031[object: org.codehaus.groovy.ast.expr.MethodCallExpression@75201592[object: org.codehaus.groovy.ast.expr.VariableExpression@7726e185[variable: featureCounts_biotype] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@aa5455e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@282308c3[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5dda14d0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1db0ec27[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d9fc57a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d4ab71a[ConstantExpression[stringtie/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b4ef7[org.codehaus.groovy.ast.expr.MethodCallExpression@1af05b03[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5987e932[object: org.codehaus.groovy.ast.expr.VariableExpression@1ad777f[variable: stringtie_log] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bbbdd4b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@438bad7c[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25230246[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fdf8f12[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a8b5227[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@54f5f647[ConstantExpression[sample_correlation_results/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6979efad[org.codehaus.groovy.ast.expr.MethodCallExpression@5a6d5a8f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a67318f[object: org.codehaus.groovy.ast.expr.VariableExpression@315ba14a[variable: sample_correlation_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@17f9344b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27f0ad19[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54e81b21[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@38d5b107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6650813a[ConstantExpression[*multiqc_report.html]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@44ea608c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50cf5a23[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@450794b4[ConstantExpression[*multiqc_data]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@273c947f[expression:ConstantExpression[
    multiqc -f .
    ]]] }]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - Apply task closure transformation to method call: org.codehaus.groovy.ast.expr.MethodCallExpression@30457e14[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[process] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@50b0bc4c[ConstantExpression[multiqc], org.codehaus.groovy.ast.expr.ClosureExpression@c20be82[]{ org.codehaus.groovy.ast.stmt.BlockStatement@13c612bd[org.codehaus.groovy.ast.stmt.ExpressionStatement@3ef41c66[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6b739528[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[publishDir] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@622ef26a[org.codehaus.groovy.ast.expr.MapExpression@41de5768[org.codehaus.groovy.ast.expr.MapEntryExpression@5f577419(key: ConstantExpression[mode], value: ConstantExpression[copy])], org.codehaus.groovy.ast.expr.GStringExpression@28fa700e[strings: [ConstantExpression[], ConstantExpression[/MultiQC]] values: [org.codehaus.groovy.ast.expr.PropertyExpression@3d526ad9[object: org.codehaus.groovy.ast.expr.VariableExpression@e041f0c[variable: params] property: ConstantExpression[outdir]]]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6a175569[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@11963225[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[memory] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3f3c966c[org.codehaus.groovy.ast.expr.ClosureExpression@11ee02f8[]{ org.codehaus.groovy.ast.stmt.BlockStatement@4102b1b1[org.codehaus.groovy.ast.stmt.ExpressionStatement@61a5b4ae[expression:org.codehaus.groovy.ast.expr.BinaryExpression@3a71c100[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@5b69fd74[org.codehaus.groovy.ast.expr.BooleanExpression@f325091 ? org.codehaus.groovy.ast.expr.PropertyExpression@437e951d[object: org.codehaus.groovy.ast.expr.VariableExpression@77b325b3[variable: params] property: ConstantExpression[multiqc_memory]] : org.codehaus.groovy.ast.expr.PropertyExpression@63a5e46c[object: ConstantExpression[4] property: ConstantExpression[GB]]]("*" at 898:46:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@7e8e8651[object: org.codehaus.groovy.ast.expr.VariableExpression@49ef32e0[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@271f18d3[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6bd51ed8[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[time] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@61e3a1fd[org.codehaus.groovy.ast.expr.ClosureExpression@51abf713[]{ org.codehaus.groovy.ast.stmt.BlockStatement@eadb475[org.codehaus.groovy.ast.stmt.ExpressionStatement@4d4d48a6[expression:org.codehaus.groovy.ast.expr.BinaryExpression@315df4bb[org.codehaus.groovy.ast.expr.ElvisOperatorExpression@3fc08eec[org.codehaus.groovy.ast.expr.BooleanExpression@5cad8b7d ? org.codehaus.groovy.ast.expr.PropertyExpression@7b02e036[object: org.codehaus.groovy.ast.expr.VariableExpression@25243bc1[variable: params] property: ConstantExpression[multiqc_time]] : org.codehaus.groovy.ast.expr.PropertyExpression@1e287667[object: ConstantExpression[4] property: ConstantExpression[h]]]("*" at 899:41:  "*" )org.codehaus.groovy.ast.expr.PropertyExpression@2e6ee0bc[object: org.codehaus.groovy.ast.expr.VariableExpression@4201a617[variable: task] property: ConstantExpression[attempt]]]]] }]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@467f77a5[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1bb9aa43[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[errorStrategy] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@420bc288[ConstantExpression[ignore]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@df5f5c0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@308a6984[object: org.codehaus.groovy.ast.expr.MethodCallExpression@66b72664[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a34b7b8[ConstantExpression[fastqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58cd06cb[org.codehaus.groovy.ast.expr.MethodCallExpression@3be8821f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@64b31700[object: org.codehaus.groovy.ast.expr.VariableExpression@3b65e559[variable: fastqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@bae47a0[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@74a9c4b0[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@85ec632[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1c05a54d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@65ef722a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5fd9b663[ConstantExpression[trimgalore/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@214894fc[org.codehaus.groovy.ast.expr.MethodCallExpression@10567255[object: org.codehaus.groovy.ast.expr.MethodCallExpression@e362c57[object: org.codehaus.groovy.ast.expr.VariableExpression@1c4ee95c[variable: trimgalore_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@79c4715d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5aa360ea[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6548bb7d[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@e27ba81[object: org.codehaus.groovy.ast.expr.MethodCallExpression@54336c81[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1556f2dd[ConstantExpression[alignment/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@35e52059[org.codehaus.groovy.ast.expr.MethodCallExpression@62577d6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bd54f7[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5f8707[variable: alignment_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@772485dd[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a12c728[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@79ab3a71[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@6e5bfdfc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d829787[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71652c98[ConstantExpression[rseqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51bde877[org.codehaus.groovy.ast.expr.MethodCallExpression@60b85ba1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@492fc69e[object: org.codehaus.groovy.ast.expr.VariableExpression@117632cf[variable: rseqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fb68ec6[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d71adc2[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@3add81c4[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1a1d3c1a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1c65121[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@159e366[ConstantExpression[preseq/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57dc9128[org.codehaus.groovy.ast.expr.MethodCallExpression@24528a25[object: org.codehaus.groovy.ast.expr.MethodCallExpression@17ae98d7[object: org.codehaus.groovy.ast.expr.VariableExpression@59221b97[variable: preseq_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ac4944a[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a772895[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@39fc6b2c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@704b2127[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3ee39da0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d332969[ConstantExpression[dupradar/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cc9ce8[org.codehaus.groovy.ast.expr.MethodCallExpression@2e27d72f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@c0b41d6[object: org.codehaus.groovy.ast.expr.VariableExpression@4837595f[variable: dupradar_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2bffa76d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b718392[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@6d2260db[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1f2d2181[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bf29c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7ee55e70[ConstantExpression[featureCounts/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fcdcf[org.codehaus.groovy.ast.expr.MethodCallExpression@7668d560[object: org.codehaus.groovy.ast.expr.MethodCallExpression@46292372[object: org.codehaus.groovy.ast.expr.VariableExpression@126be319[variable: featureCounts_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c44052e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c371e13[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@530a8454[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1e34c607[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5215cd9a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b6964d[ConstantExpression[featureCounts_biotype/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31198ceb[org.codehaus.groovy.ast.expr.MethodCallExpression@9257031[object: org.codehaus.groovy.ast.expr.MethodCallExpression@75201592[object: org.codehaus.groovy.ast.expr.VariableExpression@7726e185[variable: featureCounts_biotype] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@aa5455e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@282308c3[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@5dda14d0[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@1db0ec27[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d9fc57a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d4ab71a[ConstantExpression[stringtie/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b4ef7[org.codehaus.groovy.ast.expr.MethodCallExpression@1af05b03[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5987e932[object: org.codehaus.groovy.ast.expr.VariableExpression@1ad777f[variable: stringtie_log] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bbbdd4b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@438bad7c[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@25230246[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@4fdf8f12[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a8b5227[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@54f5f647[ConstantExpression[sample_correlation_results/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6979efad[org.codehaus.groovy.ast.expr.MethodCallExpression@5a6d5a8f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a67318f[object: org.codehaus.groovy.ast.expr.VariableExpression@315ba14a[variable: sample_correlation_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@17f9344b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27f0ad19[]]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@54e81b21[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@38d5b107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6650813a[ConstantExpression[*multiqc_report.html]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@44ea608c[expression:org.codehaus.groovy.ast.expr.MethodCallExpression@50cf5a23[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@450794b4[ConstantExpression[*multiqc_data]]]], org.codehaus.groovy.ast.stmt.ExpressionStatement@273c947f[expression:ConstantExpression[
    multiqc -f .
    ]]] }]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@308a6984[object: org.codehaus.groovy.ast.expr.MethodCallExpression@66b72664[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a34b7b8[ConstantExpression[fastqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@58cd06cb[org.codehaus.groovy.ast.expr.MethodCallExpression@3be8821f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@64b31700[object: org.codehaus.groovy.ast.expr.VariableExpression@3b65e559[variable: fastqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@bae47a0[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@74a9c4b0[]]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@66b72664[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7a34b7b8[ConstantExpression[fastqc/*]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1c05a54d[object: org.codehaus.groovy.ast.expr.MethodCallExpression@65ef722a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5fd9b663[ConstantExpression[trimgalore/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@214894fc[org.codehaus.groovy.ast.expr.MethodCallExpression@10567255[object: org.codehaus.groovy.ast.expr.MethodCallExpression@e362c57[object: org.codehaus.groovy.ast.expr.VariableExpression@1c4ee95c[variable: trimgalore_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@79c4715d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5aa360ea[]]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@65ef722a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5fd9b663[ConstantExpression[trimgalore/*]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@e27ba81[object: org.codehaus.groovy.ast.expr.MethodCallExpression@54336c81[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1556f2dd[ConstantExpression[alignment/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@35e52059[org.codehaus.groovy.ast.expr.MethodCallExpression@62577d6[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bd54f7[object: org.codehaus.groovy.ast.expr.VariableExpression@6b5f8707[variable: alignment_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@772485dd[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a12c728[]]]]
Nov-14 16:09:26.654 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@54336c81[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@1556f2dd[ConstantExpression[alignment/*]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@6e5bfdfc[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d829787[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71652c98[ConstantExpression[rseqc/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@51bde877[org.codehaus.groovy.ast.expr.MethodCallExpression@60b85ba1[object: org.codehaus.groovy.ast.expr.MethodCallExpression@492fc69e[object: org.codehaus.groovy.ast.expr.VariableExpression@117632cf[variable: rseqc_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2fb68ec6[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d71adc2[]]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3d829787[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@71652c98[ConstantExpression[rseqc/*]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1a1d3c1a[object: org.codehaus.groovy.ast.expr.MethodCallExpression@1c65121[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@159e366[ConstantExpression[preseq/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@57dc9128[org.codehaus.groovy.ast.expr.MethodCallExpression@24528a25[object: org.codehaus.groovy.ast.expr.MethodCallExpression@17ae98d7[object: org.codehaus.groovy.ast.expr.VariableExpression@59221b97[variable: preseq_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6ac4944a[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5a772895[]]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1c65121[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@159e366[ConstantExpression[preseq/*]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@704b2127[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3ee39da0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d332969[ConstantExpression[dupradar/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7cc9ce8[org.codehaus.groovy.ast.expr.MethodCallExpression@2e27d72f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@c0b41d6[object: org.codehaus.groovy.ast.expr.VariableExpression@4837595f[variable: dupradar_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@2bffa76d[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b718392[]]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3ee39da0[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5d332969[ConstantExpression[dupradar/*]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1f2d2181[object: org.codehaus.groovy.ast.expr.MethodCallExpression@49bf29c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7ee55e70[ConstantExpression[featureCounts/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3fcdcf[org.codehaus.groovy.ast.expr.MethodCallExpression@7668d560[object: org.codehaus.groovy.ast.expr.MethodCallExpression@46292372[object: org.codehaus.groovy.ast.expr.VariableExpression@126be319[variable: featureCounts_logs] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6c44052e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5c371e13[]]]]
Nov-14 16:09:26.655 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@49bf29c6[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@7ee55e70[ConstantExpression[featureCounts/*]]]
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1e34c607[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5215cd9a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b6964d[ConstantExpression[featureCounts_biotype/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@31198ceb[org.codehaus.groovy.ast.expr.MethodCallExpression@9257031[object: org.codehaus.groovy.ast.expr.MethodCallExpression@75201592[object: org.codehaus.groovy.ast.expr.VariableExpression@7726e185[variable: featureCounts_biotype] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@aa5455e[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@282308c3[]]]]
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@5215cd9a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@36b6964d[ConstantExpression[featureCounts_biotype/*]]]
Nov-14 16:09:26.657 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@1db0ec27[object: org.codehaus.groovy.ast.expr.MethodCallExpression@3d9fc57a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d4ab71a[ConstantExpression[stringtie/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@3b4ef7[org.codehaus.groovy.ast.expr.MethodCallExpression@1af05b03[object: org.codehaus.groovy.ast.expr.MethodCallExpression@5987e932[object: org.codehaus.groovy.ast.expr.VariableExpression@1ad777f[variable: stringtie_log] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@5bbbdd4b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@438bad7c[]]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@3d9fc57a[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@d4ab71a[ConstantExpression[stringtie/*]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4fdf8f12[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a8b5227[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@54f5f647[ConstantExpression[sample_correlation_results/*]]] method: ConstantExpression[from] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6979efad[org.codehaus.groovy.ast.expr.MethodCallExpression@5a6d5a8f[object: org.codehaus.groovy.ast.expr.MethodCallExpression@4a67318f[object: org.codehaus.groovy.ast.expr.VariableExpression@315ba14a[variable: sample_correlation_results] method: ConstantExpression[flatten] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@17f9344b[]] method: ConstantExpression[toList] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@27f0ad19[]]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: from
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input expression: org.codehaus.groovy.ast.expr.MethodCallExpression@4a8b5227[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@54f5f647[ConstantExpression[sample_correlation_results/*]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > input method: file
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@38d5b107[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@6650813a[ConstantExpression[*multiqc_report.html]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output expression: org.codehaus.groovy.ast.expr.MethodCallExpression@50cf5a23[object: org.codehaus.groovy.ast.expr.VariableExpression@11981797[variable: this] method: ConstantExpression[file] arguments: org.codehaus.groovy.ast.expr.ArgumentListExpression@450794b4[ConstantExpression[*multiqc_data]]]
Nov-14 16:09:26.658 [main] TRACE nextflow.ast.NextflowDSLImpl - convert > output method: file
Nov-14 16:09:27.008 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow -  NGI-RNAseq : RNA-Seq Best Practice v0.2
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - Reads          : ./data/*R{1,2}.fastq.gz
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - Genome         : GRCh37
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - Aligner        : STAR
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - Fasta Ref      : /Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta
Nov-14 16:09:27.024 [main] INFO  nextflow.Nextflow - GTF Annotation : /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Current home   : /Users/denismoreno
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Current user   : denismoreno
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Current path   : /Users/denismoreno/Documents/nextflow_test
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - R libraries    : /Users/denismoreno/R/nxtflow_libs/
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Script dir     : /Users/denismoreno/Documents/NGI-RNAseq
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Working dir    : /Users/denismoreno/Documents/nextflow_test/work
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Output dir     : ./results
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - Config Profile : docker
Nov-14 16:09:27.025 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 16:09:27.030 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: ./data/; pattern: *R{1,2}.fastq.gz; options: null
Nov-14 16:09:27.050 [Thread-1] TRACE nextflow.file.FileHelper - visitFiles > dir=; depth=0; includeDir=false; matches=false; isDir=true
Nov-14 16:09:27.051 [Thread-1] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:27.060 [Thread-1] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:27.159 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.159 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.163 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.165 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
Nov-14 16:09:27.168 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus: 8; memory: 16 GB; pollInterval: 100ms; dumpInterval: 5m
Nov-14 16:09:27.171 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
Nov-14 16:09:27.171 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Nov-14 16:09:27.173 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Nov-14 16:09:27.173 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 0
Nov-14 16:09:27.198 [main] DEBUG nextflow.Session - >>> barrier register (process: makeSTARindex)
Nov-14 16:09:27.214 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeSTARindex -- maxForks: 8
Nov-14 16:09:27.222 [main] TRACE nextflow.script.BaseParam - Creating new output channel > star_index
Nov-14 16:09:27.228 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Message arrived -- fasta => /Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta
Nov-14 16:09:27.228 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.228 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Message arrived -- $ => true
Nov-14 16:09:27.229 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.229 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Before run -- messages: [/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta, /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, true]
Nov-14 16:09:27.229 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.229 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.231 [main] DEBUG nextflow.Session - >>> barrier register (process: makeBED12)
Nov-14 16:09:27.232 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Control message arrived $ => groovyx.gpars.dataflow.operator.PoisonPill@67a99d65
Nov-14 16:09:27.232 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - Setup new process > makeSTARindex
Nov-14 16:09:27.232 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - Creating a new process > makeSTARindex
Nov-14 16:09:27.232 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: false ] -- finished: false
Nov-14 16:09:27.232 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <makeSTARindex> Poison pill arrived
Nov-14 16:09:27.233 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <makeSTARindex> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Nov-14 16:09:27.233 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: true ] -- finished: false
Nov-14 16:09:27.238 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeBED12 -- maxForks: 8
Nov-14 16:09:27.239 [main] TRACE nextflow.script.BaseParam - Creating new output channel > bed12
Nov-14 16:09:27.240 [Actor Thread 4] TRACE nextflow.processor.TaskProcessor - <makeBED12> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.241 [Actor Thread 4] TRACE nextflow.processor.TaskProcessor - <makeBED12> Message arrived -- $ => true
Nov-14 16:09:27.241 [Actor Thread 4] TRACE nextflow.processor.TaskProcessor - <makeBED12> Before run -- messages: [/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, true]
Nov-14 16:09:27.242 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Setup new process > makeBED12
Nov-14 16:09:27.242 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <makeBED12> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: false ] -- finished: false
Nov-14 16:09:27.242 [Actor Thread 4] TRACE nextflow.processor.TaskProcessor - <makeBED12> Control message arrived $ => groovyx.gpars.dataflow.operator.PoisonPill@67a99d65
Nov-14 16:09:27.243 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Creating a new process > makeBED12
Nov-14 16:09:27.243 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - <makeBED12> Poison pill arrived
Nov-14 16:09:27.243 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <makeBED12> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Nov-14 16:09:27.244 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <makeBED12> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: true ] -- finished: false
Nov-14 16:09:27.244 [Actor Thread 5] TRACE nextflow.processor.TaskContext - Binding names for 'makeBED12' > [gtf.baseName, task.memory]
Nov-14 16:09:27.244 [Actor Thread 3] TRACE nextflow.processor.TaskContext - Binding names for 'makeSTARindex' > [task.cpus]
Nov-14 16:09:27.256 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.257 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.257 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.258 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
Nov-14 16:09:27.262 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - [makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)] Store dir not set -- return false
Nov-14 16:09:27.262 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - [makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)] Store dir not set -- return false
Nov-14 16:09:27.263 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 8
Nov-14 16:09:27.263 [main] TRACE nextflow.script.BaseParam - Creating new output channel > fastqc_results
Nov-14 16:09:27.264 [Actor Thread 6] TRACE nextflow.processor.TaskProcessor - <fastqc> Message arrived -- __$setinparam<0> => [ERR458837_test, [/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, /Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz]]
Nov-14 16:09:27.264 [Actor Thread 6] TRACE nextflow.processor.TaskProcessor - <fastqc> Message arrived -- $ => true
Nov-14 16:09:27.264 [Actor Thread 6] TRACE nextflow.processor.TaskProcessor - <fastqc> Before run -- messages: [[ERR458837_test, [/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, /Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz]], true]
Nov-14 16:09:27.264 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <fastqc> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: false ] -- finished: false
Nov-14 16:09:27.265 [Actor Thread 6] TRACE nextflow.processor.TaskProcessor - <fastqc> Control message arrived __$setinparam<0> => groovyx.gpars.dataflow.operator.PoisonPill@67a99d65
Nov-14 16:09:27.265 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - Setup new process > fastqc
Nov-14 16:09:27.265 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - <fastqc> Poison pill arrived
Nov-14 16:09:27.265 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - Creating a new process > fastqc
Nov-14 16:09:27.265 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <fastqc> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Nov-14 16:09:27.265 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <fastqc> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: true ] -- finished: false
Nov-14 16:09:27.266 [Actor Thread 7] TRACE nextflow.processor.TaskContext - Binding names for 'fastqc' > [reads]
Nov-14 16:09:27.268 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.268 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.268 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.269 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_galore)
Nov-14 16:09:27.272 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - [fastqc (1)] Store dir not set -- return false
Nov-14 16:09:27.276 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 0
Nov-14 16:09:27.277 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 8
Nov-14 16:09:27.278 [main] TRACE nextflow.script.BaseParam - Creating new output channel > trimmed_reads
Nov-14 16:09:27.278 [main] TRACE nextflow.script.BaseParam - Creating new output channel > trimgalore_results
Nov-14 16:09:27.280 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <trim_galore> Message arrived -- __$setinparam<0> => [ERR458837_test, [/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, /Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz]]
Nov-14 16:09:27.280 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <trim_galore> Message arrived -- $ => true
Nov-14 16:09:27.280 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <trim_galore> Before run -- messages: [[ERR458837_test, [/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, /Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz]], true]
Nov-14 16:09:27.281 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: false ] -- finished: false
Nov-14 16:09:27.281 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <trim_galore> Control message arrived __$setinparam<0> => groovyx.gpars.dataflow.operator.PoisonPill@67a99d65
Nov-14 16:09:27.281 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - <trim_galore> Poison pill arrived
Nov-14 16:09:27.281 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - Setup new process > trim_galore
Nov-14 16:09:27.281 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - Creating a new process > trim_galore
Nov-14 16:09:27.281 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <trim_galore> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Nov-14 16:09:27.281 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: true ] -- finished: false
Nov-14 16:09:27.282 [Actor Thread 9] TRACE nextflow.processor.TaskContext - Binding names for 'trim_galore' > [tpc_r1, tpc_r2, reads, params.three_prime_clip_r1, params.three_prime_clip_r2, params.clip_r1, params.clip_r2, c_r1, c_r2, single]
Nov-14 16:09:27.282 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - [makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)] cache hash: b8ee53988d7ee272a89843411b6f50a7; mode: STANDARD; entries:
  e37c436936b580e4727c81734920a68a [java.util.UUID] 9328c5b5-b644-40a2-9ec8-4b04d87ccc75
  0cff934d12373156109276cb3e28d766 [java.lang.String] makeBED12
  964dd9a5e8344fa5092dca29df6f151b [java.lang.String]         """
        convert2bed \\
            --input=gtf \\
            --output=bed \\
            --max-mem=${task.memory.toGiga()}G \\
            < $gtf > ${gtf.baseName}.bed
        """

  f1d1b4b60efcd9b60bb2ee1df7986b3d [java.lang.String] gtf
  0d085ff13c5101abc93661c69ad36d07 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, storePath:/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, stageName:chr22.gtf)]
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true

Nov-14 16:09:27.284 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - [trim_galore (1)] Store dir not set -- return false
Nov-14 16:09:27.285 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - [fastqc (1)] cache hash: cf0cb56cc6b1e8244d074f0376f13623; mode: STANDARD; entries:
  e37c436936b580e4727c81734920a68a [java.util.UUID] 9328c5b5-b644-40a2-9ec8-4b04d87ccc75
  23037893fdd4cef8d4acc5fe82ba1899 [java.lang.String] fastqc
  9c09e002e59c547aeff894fc9fd4f2d1 [java.lang.String]     """
    fastqc -q $reads
    """

  804956c6e764ab30963d196077092d8b [java.lang.String] name
  da22c4feb2776419b802b83f24f72576 [java.lang.String] ERR458837_test
  553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  daf2b74c39777e445580d25f9ba1a0f1 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, storePath:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, stageName:ERR458837_test_R1.fastq.gz), FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz, storePath:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz, stageName:ERR458837_test_R2.fastq.gz)]
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true

Nov-14 16:09:27.285 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - [makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)] cache hash: 75e9dee391f9b86b02d6ca6e7d8149d2; mode: STANDARD; entries:
  e37c436936b580e4727c81734920a68a [java.util.UUID] 9328c5b5-b644-40a2-9ec8-4b04d87ccc75
  09696b6fc14cc76b89326ab0f815e3cc [java.lang.String] makeSTARindex
  3f3ef765ceb086c197f67257c265932f [java.lang.String]         """
        mkdir star
        STAR \\
            --runMode genomeGenerate \\
            --runThreadN ${task.cpus} \\
            --sjdbGTFfile $gtf \\
            --sjdbOverhang 149 \\
            --genomeDir star/ \\
            --genomeFastaFiles $fasta
        """

  73a5ce311a22d83f9cdf7b743bde6695 [java.lang.String] fasta
  e02e41924dfe54d485e0226b576ddf98 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta, storePath:/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta, stageName:chr22.fasta)]
  f1d1b4b60efcd9b60bb2ee1df7986b3d [java.lang.String] gtf
  0d085ff13c5101abc93661c69ad36d07 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, storePath:/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf, stageName:chr22.gtf)]
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true

Nov-14 16:09:27.286 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - [makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)] Cacheable folder: /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7 -- exists: false; try: 1
Nov-14 16:09:27.286 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - [makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)] actual run folder: null
Nov-14 16:09:27.287 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - [fastqc (1)] Cacheable folder: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623 -- exists: false; try: 1
Nov-14 16:09:27.287 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - [fastqc (1)] actual run folder: null
Nov-14 16:09:27.288 [Actor Thread 5] TRACE nextflow.processor.TaskDispatcher - Scheduling process: id: 2; name: makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf); type: SCRIPTLET; status: 2147483647; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7
Nov-14 16:09:27.288 [Actor Thread 7] TRACE nextflow.processor.TaskDispatcher - Scheduling process: id: 3; name: null; type: SCRIPTLET; status: 2147483647; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623
Nov-14 16:09:27.288 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - [makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)] Cacheable folder: /Users/denismoreno/Documents/nextflow_test/work/75/e9dee391f9b86b02d6ca6e7d8149d2 -- exists: false; try: 1
Nov-14 16:09:27.288 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - [makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)] actual run folder: null
Nov-14 16:09:27.288 [Actor Thread 3] TRACE nextflow.processor.TaskDispatcher - Scheduling process: id: 1; name: makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta); type: SCRIPTLET; status: 2147483647; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/75/e9dee391f9b86b02d6ca6e7d8149d2
Nov-14 16:09:27.290 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.290 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.290 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.292 [main] DEBUG nextflow.Session - >>> barrier register (process: star)
Nov-14 16:09:27.298 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > star -- maxForks: 8
Nov-14 16:09:27.298 [main] TRACE nextflow.script.BaseParam - Creating new output channel > star_aligned
Nov-14 16:09:27.298 [main] TRACE nextflow.script.BaseParam - Creating new output channel > alignment_logs
Nov-14 16:09:27.299 [Actor Thread 10] TRACE nextflow.processor.TaskProcessor - <star> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.299 [Actor Thread 10] TRACE nextflow.processor.TaskProcessor - <star> Message arrived -- $ => true
Nov-14 16:09:27.302 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - Task: trim_galore > Adding script vars hash code: [params.three_prime_clip_r2:0, params.three_prime_clip_r1:0, params.clip_r1:0, params.clip_r2:0]
Nov-14 16:09:27.312 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - [trim_galore (1)] cache hash: 9ff1c6ca4f5a485b6df5da79173ae2e2; mode: STANDARD; entries:
  e37c436936b580e4727c81734920a68a [java.util.UUID] 9328c5b5-b644-40a2-9ec8-4b04d87ccc75
  1656683f3c46b4418cc84eeddab9c6d2 [java.lang.String] trim_galore
  facbc1d78fc0248957fc89f942680879 [java.lang.String]     single = reads instanceof Path
    c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
    c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
    tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
    tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
    if (single) {
        """
        trim_galore --gzip $c_r1 $tpc_r1 $reads
        """
    } else {
        """
        trim_galore --paired --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $reads
        """
    }

  804956c6e764ab30963d196077092d8b [java.lang.String] name
  da22c4feb2776419b802b83f24f72576 [java.lang.String] ERR458837_test
  553096c532e666fb42214fdf0520fe4a [java.lang.String] reads
  daf2b74c39777e445580d25f9ba1a0f1 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, storePath:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R1.fastq.gz, stageName:ERR458837_test_R1.fastq.gz), FileHolder(sourceObj:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz, storePath:/Users/denismoreno/Documents/nextflow_test/data/ERR458837_test_R2.fastq.gz, stageName:ERR458837_test_R2.fastq.gz)]
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true
  20cbc75b4cab603881d1fbcd34915e2d [java.lang.String] params.three_prime_clip_r2
  bc764cd8ddf7a0cff126f51c16239658 [java.lang.Integer] 0
  4eec37abdd0ace7a2cce62a74adfc4cb [java.lang.String] params.three_prime_clip_r1
  bc764cd8ddf7a0cff126f51c16239658 [java.lang.Integer] 0
  f008b84adf9b1c7f54cbad6877fd108b [java.lang.String] params.clip_r1
  bc764cd8ddf7a0cff126f51c16239658 [java.lang.Integer] 0
  28023014fe0e5b4b24ed4e59416b44c3 [java.lang.String] params.clip_r2
  bc764cd8ddf7a0cff126f51c16239658 [java.lang.Integer] 0

Nov-14 16:09:27.312 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.313 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.313 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.313 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - [trim_galore (1)] Cacheable folder: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2 -- exists: false; try: 1
Nov-14 16:09:27.314 [main] DEBUG nextflow.Session - >>> barrier register (process: rseqc)
Nov-14 16:09:27.314 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - [trim_galore (1)] actual run folder: null
Nov-14 16:09:27.314 [Actor Thread 9] TRACE nextflow.processor.TaskDispatcher - Scheduling process: id: 4; name: null; type: SCRIPTLET; status: 2147483647; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2
Nov-14 16:09:27.320 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 8
Nov-14 16:09:27.322 [main] TRACE nextflow.script.BaseParam - Creating new output channel > rseqc_results
Nov-14 16:09:27.323 [Actor Thread 10] TRACE nextflow.processor.TaskProcessor - <rseqc> Message arrived -- $ => true
Nov-14 16:09:27.326 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.326 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.326 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.327 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq)
Nov-14 16:09:27.333 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 8
Nov-14 16:09:27.333 [main] TRACE nextflow.script.BaseParam - Creating new output channel > preseq_results
Nov-14 16:09:27.335 [Actor Thread 10] TRACE nextflow.processor.TaskProcessor - <preseq> Message arrived -- $ => true
Nov-14 16:09:27.340 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.340 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.340 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.342 [main] DEBUG nextflow.Session - >>> barrier register (process: markDuplicates)
Nov-14 16:09:27.347 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 8
Nov-14 16:09:27.348 [main] TRACE nextflow.script.BaseParam - Creating new output channel > bam_md
Nov-14 16:09:27.348 [main] TRACE nextflow.script.BaseParam - Creating new output channel > picard_results
Nov-14 16:09:27.348 [Actor Thread 10] TRACE nextflow.processor.TaskProcessor - <markDuplicates> Message arrived -- $ => true
Nov-14 16:09:27.353 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.353 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.353 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.353 [Actor Thread 9] TRACE nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -c /bin/bash -ue .command.run &> /dev/null
Nov-14 16:09:27.354 [main] DEBUG nextflow.Session - >>> barrier register (process: dupradar)
Nov-14 16:09:27.358 [Actor Thread 7] TRACE n.processor.LocalPollingMonitor - Task `fastqc (1)` cannot be scheduled -- taskCpus: 1 <= availCpus: 6 && taskMemory: 6 GB <= availMemory: 4 GB
Nov-14 16:09:27.358 [Actor Thread 9] INFO  nextflow.Session - [9f/f1c6ca] Submitted process > trim_galore (1)
Nov-14 16:09:27.358 [Actor Thread 5] TRACE n.processor.LocalPollingMonitor - Task `makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)` cannot be scheduled -- taskCpus: 1 <= availCpus: 6 && taskMemory: 16 GB <= availMemory: 4 GB
Nov-14 16:09:27.359 [Actor Thread 3] TRACE n.processor.LocalPollingMonitor - Task `makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)` cannot be scheduled -- taskCpus: 6 <= availCpus: 6 && taskMemory: 10 GB <= availMemory: 4 GB
Nov-14 16:09:27.359 [Actor Thread 9] TRACE nextflow.processor.TaskProcessor - <trim_galore> After run
Nov-14 16:09:27.359 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - <trim_galore> After stop
Nov-14 16:09:27.362 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 8
Nov-14 16:09:27.362 [main] TRACE nextflow.script.BaseParam - Creating new output channel > dupradar_results
Nov-14 16:09:27.363 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <dupradar> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.363 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <dupradar> Message arrived -- $ => true
Nov-14 16:09:27.367 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.367 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.367 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.368 [main] DEBUG nextflow.Session - >>> barrier register (process: featureCounts)
Nov-14 16:09:27.373 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 8
Nov-14 16:09:27.374 [main] TRACE nextflow.script.BaseParam - Creating new output channel > geneCounts
Nov-14 16:09:27.374 [main] TRACE nextflow.script.BaseParam - Creating new output channel > featureCounts_logs
Nov-14 16:09:27.374 [main] TRACE nextflow.script.BaseParam - Creating new output channel > featureCounts_biotype
Nov-14 16:09:27.375 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <featureCounts> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.376 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <featureCounts> Message arrived -- $ => true
Nov-14 16:09:27.379 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.385 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.385 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.385 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.386 [main] DEBUG nextflow.Session - >>> barrier register (process: stringtieFPKM)
Nov-14 16:09:27.405 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 8
Nov-14 16:09:27.407 [main] TRACE nextflow.script.BaseParam - Creating new output channel > stringtie_log
Nov-14 16:09:27.408 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <stringtieFPKM> Message arrived -- gtf => /Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf
Nov-14 16:09:27.408 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <stringtieFPKM> Message arrived -- $ => true
Nov-14 16:09:27.427 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.427 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.427 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.428 [main] DEBUG nextflow.Session - >>> barrier register (process: sample_correlation)
Nov-14 16:09:27.435 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 8
Nov-14 16:09:27.436 [main] TRACE nextflow.script.BaseParam - Creating new output channel > sample_correlation_results
Nov-14 16:09:27.436 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Message arrived -- $ => true
Nov-14 16:09:27.453 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Nov-14 16:09:27.453 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 16:09:27.453 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 16:09:27.454 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
Nov-14 16:09:27.460 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 8
Nov-14 16:09:27.462 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Nov-14 16:09:27.462 [main] DEBUG nextflow.Session - Session await
Nov-14 16:09:27.462 [Actor Thread 8] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- $ => true
Nov-14 16:09:27.479 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.579 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.683 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.787 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.893 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:27.997 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.101 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.205 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.310 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.413 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.516 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.618 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.723 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.827 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:28.930 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.030 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.135 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.239 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.344 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.447 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.550 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.651 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.755 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.860 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:29.963 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.068 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.170 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.272 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.373 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.476 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.580 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.680 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.783 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.888 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:30.992 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.097 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.202 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.306 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.410 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.515 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.619 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.724 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.825 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:31.928 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.034 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.136 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.240 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.345 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.449 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.554 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.658 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.763 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.867 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:32.972 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.076 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.181 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.285 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.390 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.494 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.599 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.702 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.808 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:33.909 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.014 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.115 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.220 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.324 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.429 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.533 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.638 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.742 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.846 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:34.951 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.056 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.160 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.265 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.369 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.474 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.578 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.681 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.783 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.888 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:35.990 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.095 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.199 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.303 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.409 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.515 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.617 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.722 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.826 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:36.931 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.035 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.137 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.240 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.343 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.447 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.552 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.656 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.761 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.865 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:37.970 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.074 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.179 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.283 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.388 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.492 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.597 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.700 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.802 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:38.906 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.010 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.115 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.218 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.322 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.427 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.531 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.636 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.740 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.845 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:39.949 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.053 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.158 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.263 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.367 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.472 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.576 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.680 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.782 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.886 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:40.989 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.093 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.197 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.302 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.406 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.511 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.615 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.720 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.824 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:41.929 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.033 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.137 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.240 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.341 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.445 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.550 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.654 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.759 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.863 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:42.968 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.070 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.175 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.275 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.380 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.484 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.589 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.693 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.798 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:43.902 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.007 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.111 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.216 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.317 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.420 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.524 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.628 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.732 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.834 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:44.935 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.040 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.145 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.249 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.353 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.458 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.562 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.667 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.771 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.876 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:45.980 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.085 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.189 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.294 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.398 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.501 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.604 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.706 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.810 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:46.915 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.019 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.124 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.228 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.330 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.434 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.536 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.641 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.745 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.849 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:47.954 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.058 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.159 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.213 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.220 [Thread-2] TRACE nextflow.processor.TaskProcessor - finalizing process > trim_galore (1) -- id: 4; name: null; type: SCRIPTLET; status: 0; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2
Nov-14 16:09:48.220 [Actor Thread 7] TRACE nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -c /bin/bash -ue .command.run &> /dev/null
Nov-14 16:09:48.221 [Actor Thread 7] INFO  nextflow.Session - [cf/0cb56c] Submitted process > fastqc (1)
Nov-14 16:09:48.221 [Actor Thread 7] TRACE nextflow.processor.TaskProcessor - <fastqc> After run
Nov-14 16:09:48.222 [Thread-2] TRACE nextflow.processor.TaskProcessor - <trim_galore> collecting output: [fileoutparam<0>:null, fileoutparam<1>:null]
Nov-14 16:09:48.222 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - <fastqc> After stop
Nov-14 16:09:48.226 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > dir=; depth=0; includeDir=true; matches=false; isDir=true
Nov-14 16:09:48.226 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.begin; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.226 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.err; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.226 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.out; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.226 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.run; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.227 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.sh; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.227 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.exitcode; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.227 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.227 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz_trimming_report.txt; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.228 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1_val_1.fq.gz; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:48.228 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.228 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz_trimming_report.txt; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.228 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2_val_2.fq.gz; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:48.231 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore (1) > after removing staged inputs: [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz]
Nov-14 16:09:48.232 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > dir=; depth=0; includeDir=true; matches=false; isDir=true
Nov-14 16:09:48.232 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.begin; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.232 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.err; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.out; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.run; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.sh; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.exitcode; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz_trimming_report.txt; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1_val_1.fq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.233 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.234 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz_trimming_report.txt; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:48.234 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2_val_2.fq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:48.234 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore (1) > after removing staged inputs: [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt]
Nov-14 16:09:48.234 [Thread-2] TRACE nextflow.processor.TaskProcessor - Finalize process > trim_galore (1)
Nov-14 16:09:48.235 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore > collecting out param: fileoutparam<0> = [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz]
Nov-14 16:09:48.235 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore > collecting out param: fileoutparam<1> = [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt]
Nov-14 16:09:48.235 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore > Binding out param: fileoutparam<0> = [[/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz]]
Nov-14 16:09:48.235 [Thread-2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Binding param fileoutparam<0> with [[/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz]]
Nov-14 16:09:48.236 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process trim_galore > Binding out param: fileoutparam<1> = [[/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt]]
Nov-14 16:09:48.236 [Thread-2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Binding param fileoutparam<1> with [[/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt]]
Nov-14 16:09:48.239 [Actor Thread 6] TRACE nextflow.processor.TaskProcessor - <star> Message arrived -- reads => [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz]
Nov-14 16:09:48.255 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1_val_1.fq.gz -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/trim_galore/ERR458837_test_R1_val_1.fq.gz
Nov-14 16:09:48.255 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Process state changed to: StateObj[submitted: 1; completed: 1; poisoned: true ] -- finished: true
Nov-14 16:09:48.255 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <trim_galore> Sending poison pills and terminating process
Nov-14 16:09:48.256 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <trim_galore> Sending a poison pill(s)
Nov-14 16:09:48.257 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: trim_galore)
Nov-14 16:09:48.259 [Actor Thread 12] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- trimgalore/* => [/Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt, /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt]
Nov-14 16:09:48.264 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2_val_2.fq.gz -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/trim_galore/ERR458837_test_R2_val_2.fq.gz
Nov-14 16:09:48.267 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R1.fastq.gz_trimming_report.txt -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/trim_galore/ERR458837_test_R1.fastq.gz_trimming_report.txt
Nov-14 16:09:48.268 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/9f/f1c6ca4f5a485b6df5da79173ae2e2/ERR458837_test_R2.fastq.gz_trimming_report.txt -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/trim_galore/ERR458837_test_R2.fastq.gz_trimming_report.txt
Nov-14 16:09:48.269 [Actor Thread 11] TRACE nextflow.processor.TaskHandler - task stats: trim_galore (1); start: 1479136167480; complete: 1479136188213; realtime: 20733 [20733];
Nov-14 16:09:48.315 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.353 [Actor Thread 11] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: ERR458837_test_R1.fastq.gz
Nov-14 16:09:48.353 [Actor Thread 11] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: ERR458837_test_R2.fastq.gz
Nov-14 16:09:48.418 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.522 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.624 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.728 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.830 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:48.935 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.039 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.144 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.244 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.347 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.451 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.554 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.657 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.759 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.864 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:49.967 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.073 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.176 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.279 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.381 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.486 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.589 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.694 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.798 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:50.900 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.005 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.106 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.210 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.315 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.419 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.521 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.625 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.726 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.828 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:51.930 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.035 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.139 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.239 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.342 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.447 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.551 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.656 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.760 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.865 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:52.969 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.074 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.178 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.283 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.387 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.492 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.592 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.695 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.799 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:53.904 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.008 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.113 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.217 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.322 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.425 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.525 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.629 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.734 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.838 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:54.940 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.043 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.147 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.251 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.355 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.459 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.559 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.664 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.767 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.872 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:55.976 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.080 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.182 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.199 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.200 [Thread-2] TRACE nextflow.processor.TaskProcessor - finalizing process > fastqc (1) -- id: 3; name: null; type: SCRIPTLET; status: 0; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623
Nov-14 16:09:56.200 [Actor Thread 5] TRACE nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -c /bin/bash -ue .command.run &> /dev/null
Nov-14 16:09:56.200 [Thread-2] TRACE nextflow.processor.TaskProcessor - <fastqc> collecting output: [fileoutparam<0>:null]
Nov-14 16:09:56.201 [Actor Thread 5] INFO  nextflow.Session - [b8/ee5398] Submitted process > makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > dir=; depth=0; includeDir=true; matches=false; isDir=true
Nov-14 16:09:56.201 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - <makeBED12> After run
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.begin; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - <makeBED12> After stop
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.err; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.out; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.run; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.command.sh; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=.exitcode; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.201 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1_fastqc.html; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:56.202 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R1_fastqc.zip; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:56.202 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2.fastq.gz; includeFile=true; matches=false; isRegularFile=true
Nov-14 16:09:56.202 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2_fastqc.html; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:56.202 [Thread-2] TRACE nextflow.file.FileHelper - visitFiles > file=ERR458837_test_R2_fastqc.zip; includeFile=true; matches=true; isRegularFile=true
Nov-14 16:09:56.203 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process fastqc (1) > after removing staged inputs: [/Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip]
Nov-14 16:09:56.203 [Thread-2] TRACE nextflow.processor.TaskProcessor - Finalize process > fastqc (1)
Nov-14 16:09:56.203 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process fastqc > collecting out param: fileoutparam<0> = [/Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip]
Nov-14 16:09:56.203 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process fastqc > Binding out param: fileoutparam<0> = [[/Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip]]
Nov-14 16:09:56.203 [Thread-2] TRACE nextflow.processor.TaskProcessor - <fastqc> Binding param fileoutparam<0> with [[/Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip]]
Nov-14 16:09:56.205 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/fastqc/ERR458837_test_R1_fastqc.html
Nov-14 16:09:56.205 [Actor Thread 11] TRACE nextflow.processor.TaskProcessor - <fastqc> Process state changed to: StateObj[submitted: 1; completed: 1; poisoned: true ] -- finished: true
Nov-14 16:09:56.205 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - <fastqc> Sending poison pills and terminating process
Nov-14 16:09:56.205 [Actor Thread 11] TRACE nextflow.processor.TaskProcessor - <fastqc> Sending a poison pill(s)
Nov-14 16:09:56.205 [Actor Thread 11] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
Nov-14 16:09:56.205 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- fastqc/* => [/Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html, /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip]
Nov-14 16:09:56.205 [Actor Thread 2] TRACE nextflow.processor.TaskHandler - task stats: fastqc (1); start: 1479136188315; complete: 1479136196199; realtime: 7884 [7884];
Nov-14 16:09:56.205 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R1_fastqc.zip -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/fastqc/ERR458837_test_R1_fastqc.zip
Nov-14 16:09:56.206 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.html -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/fastqc/ERR458837_test_R2_fastqc.html
Nov-14 16:09:56.207 [pool-3-thread-1] TRACE nextflow.processor.PublishDir - publishing file: /Users/denismoreno/Documents/nextflow_test/work/cf/0cb56cc6b1e8244d074f0376f13623/ERR458837_test_R2_fastqc.zip -[COPY]-> /Users/denismoreno/Documents/nextflow_test/results/fastqc/ERR458837_test_R2_fastqc.zip
Nov-14 16:09:56.208 [Actor Thread 2] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: ERR458837_test_R1.fastq.gz
Nov-14 16:09:56.208 [Actor Thread 2] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: ERR458837_test_R2.fastq.gz
Nov-14 16:09:56.302 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.406 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.510 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.615 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.716 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.818 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:56.922 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.027 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.131 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.235 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.340 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.445 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.549 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.654 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.758 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.863 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:57.967 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:58.072 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:58.140 [Thread-2] TRACE n.processor.TaskPollingMonitor - Scheduler queue size: 1
Nov-14 16:09:58.141 [Thread-2] TRACE nextflow.processor.TaskProcessor - finalizing process > makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf) -- id: 2; name: makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf); type: SCRIPTLET; status: 0; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7
Nov-14 16:09:58.141 [Actor Thread 3] TRACE nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -c /bin/bash -ue .command.run &> /dev/null
Nov-14 16:09:58.141 [Thread-2] TRACE nextflow.processor.TaskProcessor - <makeBED12> collecting output: [fileoutparam<0>:null]
Nov-14 16:09:58.141 [Actor Thread 3] INFO  nextflow.Session - [75/e9dee3] Submitted process > makeSTARindex (/Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta)
Nov-14 16:09:58.141 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - <makeSTARindex> After run
Nov-14 16:09:58.142 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <makeSTARindex> After stop
Nov-14 16:09:58.142 [Thread-2] TRACE nextflow.processor.TaskProcessor - Finalize process > makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)
Nov-14 16:09:58.142 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process makeBED12 > collecting out param: fileoutparam<0> = /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7/chr22.bed
Nov-14 16:09:58.142 [Thread-2] TRACE nextflow.processor.TaskProcessor - Process makeBED12 > Binding out param: fileoutparam<0> = [/Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7/chr22.bed]
Nov-14 16:09:58.142 [Thread-2] TRACE nextflow.processor.TaskProcessor - <makeBED12> Binding param fileoutparam<0> with [/Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7/chr22.bed]
Nov-14 16:09:58.142 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <rseqc> Message arrived -- bed12 => /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7/chr22.bed
Nov-14 16:09:58.145 [Thread-2] TRACE nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: id: 2; name: makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf); type: SCRIPTLET; status: 0; error: null; workDirectory: /Users/denismoreno/Documents/nextflow_test/work/b8/ee53988d7ee272a89843411b6f50a7
  error [java.lang.NullPointerException]: Cannot invoke method complete() on null object
Nov-14 16:09:58.151 [Thread-2] ERROR nextflow.processor.TaskProcessor - Error executing process > 'makeBED12 (/Users/denismoreno/Documents/nextflow_test/refs/chr22.gtf)'

Caused by:
  Cannot invoke method complete() on null object

java.lang.NullPointerException: Cannot invoke method complete() on null object
	at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:35)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:52)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at nextflow.processor.PublishDir.setPath(PublishDir.groovy:100)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:169)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at nextflow.processor.PublishDir.setPath(PublishDir.groovy:92)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.metaclass.MultipleSetterProperty.setProperty(MultipleSetterProperty.java:54)
	at groovy.lang.MetaClassImpl.setProperty(MetaClassImpl.java:2669)
	at groovy.lang.MetaClassImpl.setProperty(MetaClassImpl.java:3747)
	at nextflow.processor.PublishDir.setProperty(PublishDir.groovy)
	at org.codehaus.groovy.runtime.InvokerHelper.setProperty(InvokerHelper.java:195)
	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.setProperty(ScriptBytecodeAdapter.java:484)
	at nextflow.processor.PublishDir.createWithMap(PublishDir.groovy:160)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrapNoCoerce.invoke(StaticMetaMethodSite.java:151)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:102)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:206)
	at nextflow.processor.PublishDir.create(PublishDir.groovy:129)
	at nextflow.processor.TaskConfig.getPublishDir(TaskConfig.groovy:288)
	at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1159)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:1950)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:1921)
	at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:438)
	at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:394)
	at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:340)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:923)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:906)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:74)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.doCall(TaskPollingMonitor.groovy:319)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.call(TaskPollingMonitor.groovy)
	at groovy.lang.Closure.run(Closure.java:495)
	at java.lang.Thread.run(Thread.java:745)
Nov-14 16:09:58.163 [Thread-2] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method complete() on null object
Nov-14 16:09:58.199 [main] DEBUG nextflow.Session - Session await > processes completed
Nov-14 16:09:58.199 [main] DEBUG nextflow.Session - Session await > done
Nov-14 16:09:58.199 [main] TRACE nextflow.Session - Session > destroying
Nov-14 16:09:58.199 [main] TRACE nextflow.Session - Shutdown: [nextflow.script.WorkflowMetadata$_closure1@4af46df3, nextflow.script.ScriptRunner$_parseScript_closure7@4158debd, nextflow.processor.TaskPollingMonitor$_start_closure5@af78c87, nextflow.processor.PublishDir$_createExecutor_closure3@773dab28]
Nov-14 16:09:58.199 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <star> After stop
Nov-14 16:09:58.222 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <rseqc> After stop
Nov-14 16:09:58.227 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <preseq> After stop
Nov-14 16:09:58.230 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <markDuplicates> After stop
Nov-14 16:09:58.230 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <dupradar> After stop
Nov-14 16:09:58.230 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <featureCounts> After stop
Nov-14 16:09:58.230 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - <stringtieFPKM> After stop
Nov-14 16:09:58.234 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Message arrived -- input_files => []
Nov-14 16:09:58.234 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Before run -- messages: [[], true]
Nov-14 16:09:58.234 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Control message arrived $ => groovyx.gpars.dataflow.operator.PoisonPill@67a99d65
Nov-14 16:09:58.234 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: false ] -- finished: false
Nov-14 16:09:58.234 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <sample_correlation> Poison pill arrived
Nov-14 16:09:58.234 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Setup new process > sample_correlation
Nov-14 16:09:58.234 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Creating a new process > sample_correlation
Nov-14 16:09:58.234 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <sample_correlation> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Nov-14 16:09:58.234 [Actor Thread 2] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Process state changed to: StateObj[submitted: 1; completed: 0; poisoned: true ] -- finished: false
Nov-14 16:09:58.235 [Actor Thread 5] TRACE nextflow.processor.TaskContext - Binding names for 'sample_correlation' > [params.rlocation]
Nov-14 16:09:58.237 [main] WARN  n.processor.TaskPollingMonitor - Killing pending tasks (1)
Nov-14 16:09:58.241 [main] TRACE nextflow.executor.LocalTaskHandler - Killing process with pid: 93853
Nov-14 16:09:58.249 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - Handling error: java.lang.InterruptedException -- task: null
Nov-14 16:09:58.251 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- alignment/* => []
Nov-14 16:09:58.254 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Task sample_correlation (1) is not executed becase `when` condition is not verified
Nov-14 16:09:58.254 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - Finalize process > sample_correlation (1)
Nov-14 16:09:58.254 [Actor Thread 5] TRACE nextflow.processor.TaskProcessor - <sample_correlation> After run
Nov-14 16:09:58.254 [Actor Thread 11] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Process state changed to: StateObj[submitted: 1; completed: 1; poisoned: true ] -- finished: true
Nov-14 16:09:58.254 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - <sample_correlation> Sending poison pills and terminating process
Nov-14 16:09:58.255 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-14 16:09:58.255 [Actor Thread 2] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: /Users/denismoreno/Documents/nextflow_test/refs/chr22.fasta
Nov-14 16:09:58.255 [Actor Thread 11] TRACE nextflow.processor.TaskProcessor - <sample_correlation> Sending a poison pill(s)
Nov-14 16:09:58.255 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <sample_correlation> After stop
Nov-14 16:09:58.255 [Actor Thread 11] DEBUG nextflow.Session - <<< barrier arrive (process: sample_correlation)
Nov-14 16:09:58.256 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- sample_correlation_results/* => []
Nov-14 16:09:58.256 [main] TRACE nextflow.Session - Session > after cleanup
Nov-14 16:09:58.256 [main] TRACE nextflow.Session - Session > executor shutdown
Nov-14 16:09:58.260 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- rseqc/* => []
Nov-14 16:09:58.260 [Actor Thread 2] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: chr22.fasta
Nov-14 16:09:58.260 [Actor Thread 2] TRACE nextflow.util.PathSerializer - Path serialization > scheme: file; path: chr22.gtf
Nov-14 16:09:58.271 [Actor Thread 3] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- preseq/* => []
Nov-14 16:09:58.289 [Actor Thread 1] TRACE nextflow.processor.TaskProcessor - <multiqc> Message arrived -- dupradar/* => []
Nov-14 16:09:58.295 [main] DEBUG nextflow.Session - Session destroyed