printReads error

GATK-PrintReads-copy.cwl

#!/usr/bin/env cwl-runner

$namespaces:
  dct: http://purl.org/dc/terms/
  foaf: http://xmlns.com/foaf/0.1/
  doap: http://usefulinc.com/ns/doap#
  adms: http://www.w3.org/ns/adms#
  dcat: http://www.w3.org/ns/dcat#

$schemas:
- http://dublincore.org/2012/06/14/dcterms.rdf
- http://xmlns.com/foaf/spec/20140114.rdf
- http://usefulinc.com/ns/doap#
- http://www.w3.org/ns/adms#
- http://www.w3.org/ns/dcat.rdf

cwlVersion: "cwl:draft-3"

class: CommandLineTool

adms:includedAsset:
  doap:name: "GATK"
  doap:description: >
    The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. 
    The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.
    Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
    http://broadinstitute.github.io/picard/command-line-overview.html#MergeSamFiles
  doap:homepage: "https://www.broadinstitute.org/gatk/"
  doap:repository:
  - class: doap:GitRepository
    doap:location: "https://github.com/broadgsa/gatk.git"
  doap:release:
  - class: doap:Version
    doap:revision: "3.4"
  doap:license: "mixed licensing model"
  doap:category: "commandline tool"
  doap:programming-language: "JAVA"
  doap:developer:
  - class: foaf:Organization
    foaf:name: "Broad Institute"

description: |
  GATK-RealignTargetCreator.cwl is developed for CWL consortium
  Prints all reads that have a mapping quality above zero
    Usage: java -Xmx4g -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero

doap:name: "GATK-PrintReads.cwl"
dcat:downloadURL: "https://github.com/common-workflow-language/workflows/blob/master/tools/GATK-PrintReads.cwl"

dct:creator:
- class: foaf:Organization
  foaf:name: "THE UNIVERSITY OF MELBOURNE"
  foaf:member:
  - class: foaf:Person
    id: "farahk@student.unimelb.edu.au"
    foaf:name: "Farah Zaib Khan"
    foaf:mbox: "mailto:farahk@student.unimelb.edu.au"
    
  - class: foaf:Person
    id: "skanwal@student.unimelb.edu.au"
    foaf:name: "Sehrish Kanwal"
    foaf:mbox: "mailto:skanwal@student.unimelb.edu.au"

doap:maintainer:
- class: foaf:Organization
  foaf:name: "THE UNIVERSITY OF MELBOURNE"
  foaf:member:
  - class: foaf:Person
    id: "farahk@student.unimelb.edu.au"
    foaf:name: "Farah Zaib Khan"
    foaf:mbox: "mailto:farahk@student.unimelb.edu.au"
  - class: foaf:Person
    id: "skanwal@student.unimelb.edu.au"
    foaf:name: "Sehrish Kanwal"
    foaf:mbox: "mailto:skanwal@student.unimelb.edu.au"
    
requirements:
- $import: envvar-global.yml

hints:
 - class: DockerRequirement
   dockerPull: fzkhan/picard-1.136-gatk-2.8
   
 - class: EnvVarRequirement
   envDef: 
     - envName: CLASSPATH
       envValue: /home/biodocker/bin/GenomeAnalysisTK-2.8-1-g932cd3a/

inputs:

  - id: "#java_arg"
    type: string
    default: "-Xmx4g"
    inputBinding: 
      position: 1 

  - id: "#reference"
    type: File
    inputBinding:
      position: 5
      prefix: "-R"
    secondaryFiles:
      - ".amb"
      - ".ann"
      - ".bwt"
      - ".pac"
      - ".rbwt"
      - ".rpac"
      - ".rsa"
      - ".sa"
      - ".fai"
      - "^.dict"

  - id: "#inputBam_printReads"
    type: File
    description: bam file produced after indelRealigner
    inputBinding:
      position: 6 
      prefix: "-I"
    secondaryFiles:
      - "^.bai"
      
  - id: "#input_baseRecalibrator"
    type: File
    description: the recalibration table produced by BaseRecalibration
    inputBinding:
      position: 7 
      prefix: "-BQSR"
      
  - id: "#outputfile_printReads"
    type: ["null", string]
    description: name of the output file from indelRealigner
    inputBinding:
      position: 8
      prefix: "-o"

  - id: "#simplify"
    type: ["null", boolean]
    description: Erase all extra attributes in the read but keep the read group information
    inputBinding:
      position: 9
      prefix: "--simplify"
      
  - id: "#sample_name"
    description: Sample name to be included in the analysis. Can be specified multiple times.
    type:
      - "null"
      - type: array
        items: string
        inputBinding: { prefix: "--sample_name" }
    inputBinding: 
      position: 10
           
  - id: "#sample_file"
    type:
      - "null"
      - type: array
        items: File
        inputBinding: { prefix: "--sample_file" }
    inputBinding: 
      position: 11

  - id: "#readGroup"
    type: ["null", string]
    description: Exclude all reads with this read group from the output
    inputBinding:
      position: 12
      prefix: "--readGroup"

  - id: "#platform"
    type: ["null", string]
    description: Exclude all reads with this platform from the output
    inputBinding:
      position: 13
      prefix: "--platform"

  - id: "#number"
    type: ["null", string]
    description: Exclude all reads with this platform from the output
    inputBinding:
      position: 13
      prefix: "--number"

outputs:
  - id: "#output_printReads"
    type: File
    outputBinding: 
      glob: $(inputs.outputfile_printReads)


arguments:
  - valueFrom: "/tmp"
    position: 2
    separate: false
    prefix: "-Djava.io.tmpdir="

  - valueFrom: "PrintReads"
    position: 3
    prefix: "-T"


baseCommand: [java, org.broadinstitute.sting.gatk.CommandLineGATK]

GATK-PrintReads.json

inputBam_printReads:
  class: File
  path: "../tools/indelRealigner-2016-03-07.bam"
reference:
  class: File
  path: "../tools/outputFiles/hg19.fasta"
input_baseRecalibrator:
  class: File
  path: "../tools/baseRecalibrator-2016-03-07.table"
outputfile_printReads: printReads-2016-25-07.bam