Created
March 4, 2019 12:26
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cwltool --pack https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/3cb464a3a5c39cc060cd23d9c60918bc9ffb169b/workflows/bamfastq_align/etl.cwl
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| "fields": [ | |
| { | |
| "name": "#readgroup.yml/readgroup_fastq_se_uuid/fastq_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#readgroup.yml/readgroup_fastq_se_uuid/fastq_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "name": "#readgroup.yml/readgroup_fastq_se_uuid/readgroup_meta", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#readgroup.yml/readgroups_bam_uuid", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "#readgroup.yml/readgroups_bam_uuid/bam_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#readgroup.yml/readgroups_bam_uuid/bam_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "name": "#readgroup.yml/readgroups_bam_uuid/readgroup_meta_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_meta" | |
| } | |
| } | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "ShellCommandRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": "$(inputs.thread_count)", | |
| "coresMax": "$(inputs.thread_count)", | |
| "ramMin": 10000, | |
| "ramMax": 10000, | |
| "tmpdirMin": "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "tmpdirMax": "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "outdirMin": "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "outdirMax": "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#bwa_record_pe.cwl/fastq1", | |
| "type": "File", | |
| "format": "#bwa_record_pe.cwl/format_2182" | |
| }, | |
| { | |
| "id": "#bwa_record_pe.cwl/fastq2", | |
| "type": "File", | |
| "format": "#bwa_record_pe.cwl/format_2182" | |
| }, | |
| { | |
| "id": "#bwa_record_pe.cwl/fasta", | |
| "type": "File", | |
| "format": "#bwa_record_pe.cwl/format_1929", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_record_pe.cwl/readgroup_meta", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "id": "#bwa_record_pe.cwl/fastqc_json_path", | |
| "type": "File", | |
| "format": "#bwa_record_pe.cwl/format_3464", | |
| "inputBinding": { | |
| "loadContents": true, | |
| "valueFrom": "$(null)" | |
| } | |
| }, | |
| { | |
| "id": "#bwa_record_pe.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#bwa_record_pe.cwl/OUTPUT", | |
| "type": "File", | |
| "format": "#bwa_record_pe.cwl/format_2572", | |
| "outputBinding": { | |
| "glob": "$(inputs.readgroup_meta['ID'] + \".bam\")" | |
| } | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "${\n function to_rg() {\n var readgroup_str = \"@RG\";\n var keys = Object.keys(inputs.readgroup_meta).sort();\n for (var i = 0; i < keys.length; i++) {\n var key = keys[i];\n var value = inputs.readgroup_meta[key];\n if (key.length == 2 && value != null) {\n readgroup_str = readgroup_str + \"\\\\t\" + key + \":\" + value;\n }\n }\n return readgroup_str\n }\n\n function bwa_aln_33(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"aln\", \"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq1.path, \">\", \"aln.sai1\", \"&&\",\n \"bwa\", \"aln\", \"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq2.path, \">\", \"aln.sai2\", \"&&\",\n \"bwa\", \"sampe\", \"-r\", \"\\\"\" + rg_str + \"\\\"\", inputs.fasta.path, \"aln.sai1\", \"aln.sai2\", inputs.fastq1.path, inputs.fastq2.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n function bwa_aln_64(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"aln\", \"-I\",\"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq1.path, \">\", \"aln.sai1\", \"&&\",\n \"bwa\", \"aln\", \"-I\", \"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq2.path, \">\", \"aln.sai2\", \"&&\",\n \"bwa\", \"sampe\", \"-r\", \"\\\"\" + rg_str + \"\\\"\", inputs.fasta.path, \"aln.sai1\", \"aln.sai2\", inputs.fastq1.path, inputs.fastq2.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n function bwa_mem(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"mem\", \"-t\", inputs.thread_count, \"-T\", \"0\", \"-R\", \"\\\"\" + rg_str + \"\\\"\",\n inputs.fasta.path, inputs.fastq1.path, inputs.fastq2.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n var MEM_ALN_CUTOFF = 70;\n var fastqc_json = JSON.parse(inputs.fastqc_json_path.contents);\n var readlength = fastqc_json[inputs.fastq1.basename][\"Sequence length\"];\n var encoding = fastqc_json[inputs.fastq1.basename][\"Encoding\"];\n var rg_str = to_rg();\n\n var outbam = inputs.readgroup_meta['ID'] + \".bam\";\n\n if (encoding == \"Illumina 1.3\" || encoding == \"Illumina 1.5\") {\n return bwa_aln_64(rg_str, outbam)\n } else if (encoding == \"Sanger / Illumina 1.9\") {\n if (readlength < MEM_ALN_CUTOFF) {\n return bwa_aln_33(rg_str, outbam)\n }\n else {\n return bwa_mem(rg_str, outbam)\n }\n } else {\n return\n }\n\n}\n" | |
| } | |
| ], | |
| "baseCommand": [ | |
| "bash", | |
| "-c" | |
| ], | |
| "id": "#bwa_record_pe.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/bwa:6f48348ec54042c9bb420ea5e28eea8f62a81c15b44800673bdfece1f379591b" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "ShellCommandRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": "$(inputs.thread_count)", | |
| "coresMax": "$(inputs.thread_count)", | |
| "ramMin": 10000, | |
| "ramMax": 10000, | |
| "tmpdirMin": "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))", | |
| "tmpdirMax": "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))", | |
| "outdirMin": "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))", | |
| "outdirMax": "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))" | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#bwa_record_se.cwl/fastq", | |
| "type": "File", | |
| "format": "#bwa_record_se.cwl/format_2182" | |
| }, | |
| { | |
| "id": "#bwa_record_se.cwl/fasta", | |
| "type": "File", | |
| "format": "#bwa_record_se.cwl/format_1929", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_record_se.cwl/readgroup_meta", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "id": "#bwa_record_se.cwl/fastqc_json_path", | |
| "type": "File", | |
| "inputBinding": { | |
| "loadContents": true, | |
| "valueFrom": "$(null)" | |
| } | |
| }, | |
| { | |
| "id": "#bwa_record_se.cwl/samse_maxOcc", | |
| "type": "long", | |
| "default": 3 | |
| }, | |
| { | |
| "id": "#bwa_record_se.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#bwa_record_se.cwl/OUTPUT", | |
| "type": "File", | |
| "format": "#bwa_record_se.cwl/format_2572", | |
| "outputBinding": { | |
| "glob": "$(inputs.readgroup_meta['ID'] + \".bam\")" | |
| } | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "${\n function to_rg() {\n var readgroup_str = \"@RG\";\n var keys = Object.keys(inputs.readgroup_meta).sort();\n for (var i = 0; i < keys.length; i++) {\n var key = keys[i];\n var value = inputs.readgroup_meta[key];\n if (key.length == 2 && value != null) {\n readgroup_str = readgroup_str + \"\\\\t\" + key + \":\" + value;\n }\n }\n return readgroup_str\n }\n\n function bwa_aln_33(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"aln\", \"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq.path, \">\", \"aln.sai\", \"&&\",\n \"bwa\", \"samse\", \"-n\", inputs.samse_maxOcc, \"-r\", \"\\\"\" + rg_str + \"\\\"\", inputs.fasta.path, \"aln.sai\", inputs.fastq.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n function bwa_aln_64(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"aln\", \"-I\",\"-t\", inputs.thread_count, inputs.fasta.path, inputs.fastq.path, \">\", \"aln.sai\", \"&&\",\n \"bwa\", \"samse\", \"-n\", inputs.samse_maxOcc, \"-r\", \"\\\"\" + rg_str + \"\\\"\", inputs.fasta.path, \"aln.sai\", inputs.fastq.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n function bwa_mem(rg_str, outbam) {\n var cmd = [\n \"bwa\", \"mem\", \"-t\", inputs.thread_count, \"-T\", \"0\", \"-R\", \"\\\"\" + rg_str + \"\\\"\",\n inputs.fasta.path, inputs.fastq.path, \"|\",\n \"samtools\", \"view\", \"-Shb\", \"-o\", outbam, \"-\"\n ];\n return cmd.join(' ')\n }\n\n var MEM_ALN_CUTOFF = 70;\n var fastqc_json = JSON.parse(inputs.fastqc_json_path.contents);\n var readlength = fastqc_json[inputs.fastq.basename][\"Sequence length\"];\n var encoding = fastqc_json[inputs.fastq.basename][\"Encoding\"];\n var rg_str = to_rg();\n\n var outbam = inputs.readgroup_meta['ID'] + \".bam\";\n\n if (encoding == \"Illumina 1.3\" || encoding == \"Illumina 1.5\") {\n return bwa_aln_64(rg_str, outbam)\n } else if (encoding == \"Sanger / Illumina 1.9\") {\n if (readlength < MEM_ALN_CUTOFF) {\n return bwa_aln_33(rg_str, outbam)\n }\n else {\n return bwa_mem(rg_str, outbam)\n }\n } else {\n return\n }\n\n}\n" | |
| } | |
| ], | |
| "baseCommand": [ | |
| "bash", | |
| "-c" | |
| ], | |
| "id": "#bwa_record_se.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#decider_conditional_bams.cwl/conditional_bam1", | |
| "format": "#decider_conditional_bams.cwl/format_2572", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| }, | |
| { | |
| "id": "#decider_conditional_bams.cwl/conditional_sqlite1", | |
| "format": "#decider_conditional_bams.cwl/format_3621", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| }, | |
| { | |
| "id": "#decider_conditional_bams.cwl/conditional_bam2", | |
| "format": "#decider_conditional_bams.cwl/format_2572", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| }, | |
| { | |
| "id": "#decider_conditional_bams.cwl/conditional_sqlite2", | |
| "format": "#decider_conditional_bams.cwl/format_3621", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#decider_conditional_bams.cwl/output", | |
| "format": "#decider_conditional_bams.cwl/format_2572", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ] | |
| }, | |
| { | |
| "id": "#decider_conditional_bams.cwl/sqlite", | |
| "format": "#decider_conditional_bams.cwl/format_3621", | |
| "type": "File" | |
| } | |
| ], | |
| "expression": "${\n if (inputs.conditional_bam1.length == 1 && inputs.conditional_bam2.length == 0) {\n var output = inputs.conditional_bam1[0];\n var sqlite = inputs.conditional_sqlite1[0];\n }\n else if (inputs.conditional_bam1.length == 0 && inputs.conditional_bam2.length == 1) {\n var output = inputs.conditional_bam2[0];\n var sqlite = inputs.conditional_sqlite2[0];\n }\n else {\n throw \"unhandled\";\n }\n\n return {'output': output, 'sqlite': sqlite};\n }\n", | |
| "id": "#decider_conditional_bams.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#decider_readgroup_expression.cwl/fastq", | |
| "format": "#decider_readgroup_expression.cwl/format_2182", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| }, | |
| { | |
| "id": "#decider_readgroup_expression.cwl/readgroup_json", | |
| "format": "#decider_readgroup_expression.cwl/format_3464", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#decider_readgroup_expression.cwl/output", | |
| "format": "#decider_readgroup_expression.cwl/format_3464", | |
| "type": { | |
| "type": "array", | |
| "items": "File" | |
| } | |
| } | |
| ], | |
| "expression": "${\n\n // https://stackoverflow.com/a/9849276/810957\n function include(arr,obj) {\n return (arr.indexOf(obj) != -1)\n }\n\n // https://stackoverflow.com/a/2548133/810957\n function endsWith(str, suffix) {\n return str.indexOf(suffix, str.length - suffix.length) !== -1;\n }\n\n // https://stackoverflow.com/questions/3820381/need-a-basename-function-in-javascript#comment29942319_15270931\n function local_basename(path) {\n var basename = path.split(/[\\\\/]/).pop();\n return basename\n }\n\n // https://planetozh.com/blog/2008/04/javascript-basename-and-dirname/\n function local_dirname(path) {\n return path.replace(/\\\\/g,'/').replace(/\\/[^\\/]*$/, '');\n }\n\n function get_slice_number(fastq_name) {\n if (endsWith(fastq_name, '_1.fq.gz')) {\n return -8\n }\n else if (endsWith(fastq_name, '_s.fq.gz')) {\n return -8\n }\n else if (endsWith(fastq_name, '_o1.fq.gz')) {\n return -9\n }\n else if (endsWith(fastq_name, '_o2.fq.gz')) {\n return -9\n }\n else {\n throw \"not recognized fastq suffix\"\n }\n }\n \n // get predicted readgroup basenames from fastq\n var readgroup_basename_array = [];\n for (var i = 0; i < inputs.fastq.length; i++) {\n var fq_path = inputs.fastq[i];\n var fq_name = local_basename(fq_path.location);\n\n var slice_number = get_slice_number(fq_name);\n \n var readgroup_name = fq_name.slice(0,slice_number) + \".json\";\n readgroup_basename_array.push(readgroup_name);\n }\n\n // find which readgroup items are in predicted basenames\n var readgroup_array = [];\n for (var i = 0; i < inputs.readgroup_json.length; i++) {\n var readgroup = inputs.readgroup_json[i];\n var readgroup_basename = local_basename(readgroup.location);\n if (include(readgroup_basename_array, readgroup_basename)) {\n readgroup_array.push(readgroup);\n }\n }\n\n var readgroup_sorted = readgroup_array.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) });\n return {'output': readgroup_sorted}\n }\n", | |
| "id": "#decider_readgroup_expression.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_file", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_file/amplicon_kit_amplicon_file", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_file/amplicon_kit_target_file", | |
| "type": "File" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_uuid", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_uuid/amplicon_kit_amplicon_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_uuid/amplicon_kit_amplicon_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_uuid/amplicon_kit_target_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#amplicon_kit.yml/amplicon_kit_set_uuid/amplicon_kit_target_file_size", | |
| "type": "long" | |
| } | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_amplicon_kit_file.cwl/amplicon_kit_amplicon_file", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_amplicon_kit_file.cwl/amplicon_kit_target_file", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_amplicon_kit_file.cwl/output", | |
| "type": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| } | |
| ], | |
| "expression": "${\n var output = {'amplicon_kit_amplicon_file': inputs.amplicon_kit_amplicon_file,\n 'amplicon_kit_target_file': inputs.amplicon_kit_target_file};\n return {'output': output};\n}\n", | |
| "id": "#emit_amplicon_kit_file.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_file", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_file/capture_kit_bait_file", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_file/capture_kit_target_file", | |
| "type": "File" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_uuid", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_uuid/capture_kit_bait_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_uuid/capture_kit_bait_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_uuid/capture_kit_target_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#capture_kit.yml/capture_kit_set_uuid/capture_kit_target_file_size", | |
| "type": "long" | |
| } | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_capture_kit_file.cwl/capture_kit_bait_file", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_capture_kit_file.cwl/capture_kit_target_file", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_capture_kit_file.cwl/output", | |
| "type": "#capture_kit.yml/capture_kit_set_file" | |
| } | |
| ], | |
| "expression": "${\n var output = {'capture_kit_bait_file': inputs.capture_kit_bait_file,\n 'capture_kit_target_file': inputs.capture_kit_target_file};\n return {'output': output};\n}\n", | |
| "id": "#emit_capture_kit_file.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_file_format.cwl/input", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_file_format.cwl/format", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_file_format.cwl/output", | |
| "type": "File" | |
| } | |
| ], | |
| "expression": "${\n var output = inputs.input;\n output.format = inputs.format;\n return {'output': output}\n}\n", | |
| "id": "#emit_file_format.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_json_readgroup_meta.cwl/input", | |
| "type": "File", | |
| "inputBinding": { | |
| "loadContents": true, | |
| "valueFrom": "$(null)" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_json_readgroup_meta.cwl/output", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| } | |
| ], | |
| "expression": "${\n var readgroup = JSON.parse(inputs.input.contents);\n var output = new Object();\n for (var i in readgroup) {\n if (i.length == 2) {\n if (i == 'PL') {\n output[i] = readgroup[i].toUpperCase();\n } else {\n output[i] = readgroup[i];\n }\n }\n }\n\n return {'output': output};\n}\n", | |
| "id": "#emit_json_readgroup_meta.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_json_value.cwl/input", | |
| "type": "File", | |
| "inputBinding": { | |
| "loadContents": true, | |
| "valueFrom": "$(null)" | |
| } | |
| }, | |
| { | |
| "id": "#emit_json_value.cwl/key", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_json_value.cwl/output", | |
| "type": "string" | |
| } | |
| ], | |
| "expression": "${\n var output_value = JSON.parse(inputs.input.contents)[inputs.key];\n return {'output': output_value};\n}\n", | |
| "id": "#emit_json_value.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_readgroup_fastq_pe_file.cwl/forward_fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_readgroup_fastq_pe_file.cwl/reverse_fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_readgroup_fastq_pe_file.cwl/readgroup_meta", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_readgroup_fastq_pe_file.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file" | |
| } | |
| ], | |
| "expression": "${\n var output = { \"forward_fastq\": inputs.forward_fastq,\n \"reverse_fastq\": inputs.reverse_fastq,\n \"readgroup_meta\": inputs.readgroup_meta\n };\n output.forward_fastq.format = \"edam:format_2182\";\n output.reverse_fastq.format = \"edam:format_2182\";\n return {'output': output}\n}\n", | |
| "id": "#emit_readgroup_fastq_pe_file.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_readgroup_fastq_se_file.cwl/fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_readgroup_fastq_se_file.cwl/readgroup_meta", | |
| "type": "#readgroup.yml/readgroup_meta" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_readgroup_fastq_se_file.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file" | |
| } | |
| ], | |
| "expression": "${\n var output = { \"fastq\": inputs.fastq,\n \"readgroup_meta\": inputs.readgroup_meta};\n output.fastq.format = \"edam:format_2182\";\n return {'output': output}\n}\n", | |
| "id": "#emit_readgroup_fastq_se_file.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#emit_readgroups_bam_file.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#emit_readgroups_bam_file.cwl/readgroup_meta_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_meta" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#emit_readgroups_bam_file.cwl/output", | |
| "type": "#readgroup.yml/readgroups_bam_file" | |
| } | |
| ], | |
| "expression": "${\n var output = { \"bam\": inputs.bam,\n \"readgroup_meta_list\": inputs.readgroup_meta_list};\n output.bam.format = \"edam:format_2572\";\n return {'output': output}\n}\n", | |
| "id": "#emit_readgroups_bam_file.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/fastq_cleaner:428dc9a83e62a74c61d8a5fe907f5d75154f862dc47b755b0f7cfdf1cfd66668" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 2, | |
| "coresMax": 2, | |
| "ramMin": 2000, | |
| "ramMax": 2000, | |
| "tmpdirMin": "$(Math.ceil(1.1 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "tmpdirMax": "$(Math.ceil(1.1 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "outdirMin": "$(Math.ceil(1.1 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))", | |
| "outdirMax": "$(Math.ceil(1.1 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/fastq1", | |
| "type": "File", | |
| "format": "#fastq_cleaner_pe.cwl/format_2182", | |
| "inputBinding": { | |
| "prefix": "--fastq" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/fastq2", | |
| "type": "File", | |
| "format": "#fastq_cleaner_pe.cwl/format_2182", | |
| "inputBinding": { | |
| "prefix": "--fastq2" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/reads_in_memory", | |
| "type": "long", | |
| "default": 500000, | |
| "inputBinding": { | |
| "prefix": "--reads_in_memory" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/cleaned_fastq1", | |
| "type": "File", | |
| "format": "#fastq_cleaner_pe.cwl/format_2182", | |
| "outputBinding": { | |
| "glob": "$(inputs.fastq1.basename)" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/cleaned_fastq2", | |
| "type": "File", | |
| "format": "#fastq_cleaner_pe.cwl/format_2182", | |
| "outputBinding": { | |
| "glob": "$(inputs.fastq2.basename)" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_pe.cwl/result_json", | |
| "type": "File", | |
| "format": "#fastq_cleaner_pe.cwl/format_3464", | |
| "outputBinding": { | |
| "glob": "result.json" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/fastq_cleaner" | |
| ], | |
| "id": "#fastq_cleaner_pe.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/fastq_cleaner:428dc9a83e62a74c61d8a5fe907f5d75154f862dc47b755b0f7cfdf1cfd66668" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 2000, | |
| "ramMax": 2000, | |
| "tmpdirMin": "$(Math.ceil(1.1 * inputs.fastq.size / 1048576))", | |
| "tmpdirMax": "$(Math.ceil(1.1 * inputs.fastq.size / 1048576))", | |
| "outdirMin": "$(Math.ceil(1.1 * inputs.fastq.size / 1048576))", | |
| "outdirMax": "$(Math.ceil(1.1 * inputs.fastq.size / 1048576))" | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#fastq_cleaner_se.cwl/fastq", | |
| "type": "File", | |
| "format": "#fastq_cleaner_se.cwl/format_2182", | |
| "inputBinding": { | |
| "prefix": "--fastq" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_se.cwl/reads_in_memory", | |
| "type": "long", | |
| "default": 500000, | |
| "inputBinding": { | |
| "prefix": "--reads_in_memory" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastq_cleaner_se.cwl/cleaned_fastq", | |
| "type": "File", | |
| "format": "#fastq_cleaner_se.cwl/format_2182", | |
| "outputBinding": { | |
| "glob": "$(inputs.fastq.basename)" | |
| } | |
| }, | |
| { | |
| "id": "#fastq_cleaner_se.cwl/result_json", | |
| "type": "File", | |
| "format": "#fastq_cleaner_se.cwl/format_3464", | |
| "outputBinding": { | |
| "glob": "result.json" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/fastq_cleaner" | |
| ], | |
| "id": "#fastq_cleaner_se.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/fastqc:27ec215ea82bd62a76ec86f9c8a692010cc0c99169e68d2fa0c0052450321f57" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": "$(inputs.threads)", | |
| "coresMax": "$(inputs.threads)", | |
| "ramMin": 5000, | |
| "ramMax": 5000, | |
| "tmpdirMin": 50, | |
| "tmpdirMax": 50, | |
| "outdirMin": 5, | |
| "outdirMax": 5 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#fastqc.cwl/adapters", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--adapters" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/casava", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--casava" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/contaminants", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--contaminants" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/dir", | |
| "type": "string", | |
| "default": ".", | |
| "inputBinding": { | |
| "prefix": "--dir" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/extract", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--extract" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/format", | |
| "type": "string", | |
| "default": "fastq", | |
| "inputBinding": { | |
| "prefix": "--format" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/INPUT", | |
| "type": "File", | |
| "format": "#fastqc.cwl/format_2182", | |
| "inputBinding": { | |
| "position": 99 | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/kmers", | |
| "type": "long", | |
| "default": 7, | |
| "inputBinding": { | |
| "prefix": "--kmers" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/limits", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "--limits" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/nano", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--nano" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/noextract", | |
| "type": "boolean", | |
| "default": true, | |
| "inputBinding": { | |
| "prefix": "--noextract" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/nofilter", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--nofilter" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/nogroup", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--nogroup" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/outdir", | |
| "type": "string", | |
| "default": ".", | |
| "inputBinding": { | |
| "prefix": "--outdir" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/quiet", | |
| "type": "boolean", | |
| "default": false, | |
| "inputBinding": { | |
| "prefix": "--quiet" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc.cwl/threads", | |
| "type": "long", | |
| "default": 1, | |
| "inputBinding": { | |
| "prefix": "--threads" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastqc.cwl/OUTPUT", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "*_fastqc.zip" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/FastQC/fastqc" | |
| ], | |
| "id": "#fastqc.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/fastqc_to_json:0ebd446f08d9eb6ed5b069e9ae53ad822236dc56bb1154f9df0e0c22b5724ae7" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 1000, | |
| "ramMax": 1000, | |
| "tmpdirMin": 1, | |
| "tmpdirMax": 1, | |
| "outdirMin": 1, | |
| "outdirMax": 1 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#fastqc_basicstatistics_json.cwl/sqlite_path", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "--sqlite_path" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastqc_basicstatistics_json.cwl/OUTPUT", | |
| "type": "File", | |
| "format": "#fastqc_basicstatistics_json.cwl/format_3464", | |
| "outputBinding": { | |
| "glob": "fastqc.json" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/fastqc_to_json" | |
| ], | |
| "id": "#fastqc_basicstatistics_json.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/fastqc_db:3383ae9c9beaf905682b21cab14d20b3bc4fc738c7e1e126da99dc288ba016ac" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 1000, | |
| "ramMax": 1000, | |
| "tmpdirMin": 100, | |
| "tmpdirMax": 100, | |
| "outdirMin": 10, | |
| "outdirMax": 10 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#fastqc_db.cwl/INPUT", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "--INPUT" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc_db.cwl/job_uuid", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "--job_uuid" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastqc_db.cwl/LOG", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.job_uuid + \".log\")" | |
| } | |
| }, | |
| { | |
| "id": "#fastqc_db.cwl/OUTPUT", | |
| "type": "File", | |
| "format": "#fastqc_db.cwl/format_3621", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".db\")" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/fastqc_db" | |
| ], | |
| "id": "#fastqc_db.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
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| { | |
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| "class": "CommandLineTool", | |
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| { | |
| "id": "#gatk4_applybqsr.cwl/input", | |
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| "prefix": "--input" | |
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| "^.bai" | |
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| }, | |
| { | |
| "id": "#gatk4_applybqsr.cwl/bqsr-recal-file", | |
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| { | |
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| { | |
| "id": "#gatk4_applybqsr.cwl/output_bam", | |
| "format": "#gatk4_applybqsr.cwl/format_2572", | |
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| { | |
| "valueFrom": "$(inputs.input.basename)", | |
| "prefix": "--output" | |
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| ], | |
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| "/usr/local/bin/gatk-package-4.0.7.0-local.jar", | |
| "ApplyBQSR" | |
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| "id": "#gatk4_applybqsr.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
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| { | |
| "id": "#gatk4_baserecalibrator.cwl/input", | |
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| "prefix": "--input" | |
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| "^.bai" | |
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| { | |
| "id": "#gatk4_baserecalibrator.cwl/known-sites", | |
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| ".tbi" | |
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| { | |
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| { | |
| "id": "#gatk4_baserecalibrator.cwl/output_grp", | |
| "type": "File", | |
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| "glob": "$(inputs.input.nameroot + \"_bqsr.grp\")" | |
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| "valueFrom": "$(inputs.input.nameroot + \"_bqsr.grp\")", | |
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| "id": "#gatk4_baserecalibrator.cwl" | |
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| { | |
| "class": "DockerRequirement", | |
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| { | |
| "id": "#gatk4_calculatecontamination.cwl/input", | |
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| "prefix": "--input" | |
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| }, | |
| { | |
| "id": "#gatk4_calculatecontamination.cwl/TMP_DIR", | |
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| { | |
| "id": "#gatk4_calculatecontamination.cwl/bam_nameroot", | |
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| "id": "#gatk4_calculatecontamination.cwl/output", | |
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| "class": "DockerRequirement", | |
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| { | |
| "id": "#gatk4_getpileupsummaries.cwl/input", | |
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| "prefix": "--input" | |
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| "^.bai" | |
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| { | |
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| { | |
| "class": "DockerRequirement", | |
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| { | |
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| }, | |
| { | |
| "id": "#gatk_calculatecontamination_to_sqlite.cwl/input_state", | |
| "type": "string", | |
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| "prefix": "--input_state" | |
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| { | |
| "id": "#gatk_calculatecontamination_to_sqlite.cwl/job_uuid", | |
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| { | |
| "id": "#gatk_calculatecontamination_to_sqlite.cwl/metric_path", | |
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| { | |
| "id": "#gatk_calculatecontamination_to_sqlite.cwl/log", | |
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| "id": "#gatk_calculatecontamination_to_sqlite.cwl/sqlite", | |
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| { | |
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| "prefix": "--md5sum_path" | |
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| "prefix": "--sha256sum_path" | |
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| "glob": "$(inputs.job_uuid + \".log\")" | |
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| "glob": "$(inputs.job_uuid + \".db\")" | |
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| "prefix": "--input_json" | |
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| "prefix": "--job_uuid" | |
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| }, | |
| { | |
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| "prefix": "--table_name" | |
| } | |
| } | |
| ], | |
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| { | |
| "id": "#json_to_sqlite.cwl/sqlite", | |
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| "type": "File", | |
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| "glob": "$(inputs.job_uuid).db" | |
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| "glob": "$(inputs.job_uuid).log" | |
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| { | |
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| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "ubuntu:bionic-20180426" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
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| "class": "CommandLineTool", | |
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| "id": "#ls_l.cwl/INPUT", | |
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| "position": 0 | |
| } | |
| } | |
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| { | |
| "id": "#ls_l.cwl/OUTPUT", | |
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| "glob": "$(inputs.INPUT.nameroot + \".ls\")" | |
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| } | |
| ], | |
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| "id": "#ls_l.cwl" | |
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| { | |
| "class": "DockerRequirement", | |
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| { | |
| "class": "InlineJavascriptRequirement" | |
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| ], | |
| "class": "CommandLineTool", | |
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| { | |
| "id": "#md5sum.cwl/INPUT", | |
| "type": "File", | |
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| "position": 0 | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#md5sum.cwl/OUTPUT", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".md5\")" | |
| } | |
| } | |
| ], | |
| "stdout": "$(inputs.INPUT.nameroot + \".md5\")", | |
| "baseCommand": [ | |
| "md5sum" | |
| ], | |
| "id": "#md5sum.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
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| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
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| } | |
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| "class": "ExpressionTool", | |
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| { | |
| "id": "#merge_pe_fastq_records.cwl/input", | |
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| "type": "array", | |
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| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_pe_file" | |
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| "outputs": [ | |
| { | |
| "id": "#merge_pe_fastq_records.cwl/output", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_pe_file" | |
| } | |
| } | |
| ], | |
| "expression": "${\n var output = [];\n var readgroup_array_str = \"\";\n for (var i = 0; i < inputs.input.length; i++) {\n var readgroup_array = inputs.input[i];\n readgroup_array_str += \" \" + readgroup_array;\n for (var j = 0; j < readgroup_array.length; j++) {\n var readgroup = readgroup_array[j];\n output.push(readgroup);\n }\n }\n\n return {'output': output}\n}\n", | |
| "id": "#merge_pe_fastq_records.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
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| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
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| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "ExpressionTool", | |
| "inputs": [ | |
| { | |
| "id": "#merge_se_fastq_records.cwl/input", | |
| "type": { | |
| "type": "array", | |
| "items": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| } | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#merge_se_fastq_records.cwl/output", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| } | |
| } | |
| ], | |
| "expression": "${\n var output = [];\n var readgroup_array_str = \"\";\n for (var i = 0; i < inputs.input.length; i++) {\n var readgroup_array = inputs.input[i];\n readgroup_array_str += \" \" + readgroup_array;\n for (var j = 0; j < readgroup_array.length; j++) {\n var readgroup = readgroup_array[j];\n output.push(readgroup);\n }\n }\n\n return {'output': output}\n}\n", | |
| "id": "#merge_se_fastq_records.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/merge_sqlite:1b3a6f55be8579ecfb4c9c0513c3b710717a8f4cd8e79c88ee8c0f28f604faa3" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 1000, | |
| "ramMax": 1000, | |
| "tmpdirMin": "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(2 * (req_space / 1048576));\n} \n", | |
| "tmpdirMax": "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(2 * (req_space / 1048576));\n} \n", | |
| "outdirMin": "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n} \n", | |
| "outdirMax": "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#merge_sqlite.cwl/source_sqlite", | |
| "format": "#merge_sqlite.cwl/format_3621", | |
| "type": { | |
| "type": "array", | |
| "items": "File", | |
| "inputBinding": { | |
| "prefix": "--source_sqlite" | |
| } | |
| } | |
| }, | |
| { | |
| "id": "#merge_sqlite.cwl/job_uuid", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "--job_uuid" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#merge_sqlite.cwl/destination_sqlite", | |
| "format": "#merge_sqlite.cwl/format_3621", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.job_uuid + \".db\")" | |
| } | |
| }, | |
| { | |
| "id": "#merge_sqlite.cwl/log", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.job_uuid + \".log\")" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/merge_sqlite" | |
| ], | |
| "id": "#merge_sqlite.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/picard:092d034713aff237cf07ef28c22a46a113d1a59dc7ec6d71beb72295044a46f8" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 49152, | |
| "ramMax": 49152, | |
| "tmpdirMin": 1000, | |
| "tmpdirMax": 1000, | |
| "outdirMin": 1000, | |
| "outdirMax": 1000 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/BAIT_INTERVALS", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "BAIT_INTERVALS=", | |
| "position": 10, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/BAIT_SET_NAME", | |
| "type": [ | |
| "null", | |
| "string" | |
| ], | |
| "inputBinding": { | |
| "prefix": "BAIT_SET_NAME=", | |
| "position": 11, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/CLIP_OVERLAPPING_READS", | |
| "type": "string", | |
| "default": "true", | |
| "inputBinding": { | |
| "prefix": "CLIP_OVERLAPPING_READS=", | |
| "position": 12, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/COVERAGE_CAP", | |
| "type": "int", | |
| "default": 200, | |
| "inputBinding": { | |
| "prefix": "COVERAGE_CAP=", | |
| "position": 13, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/INPUT", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "INPUT=", | |
| "position": 14, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/METRIC_ACCUMULATION_LEVEL", | |
| "type": { | |
| "type": "array", | |
| "items": "string", | |
| "inputBinding": { | |
| "prefix": "METRIC_ACCUMULATION_LEVEL=", | |
| "position": 15, | |
| "separate": false | |
| } | |
| }, | |
| "default": [ | |
| "ALL_READS", | |
| "LIBRARY", | |
| "SAMPLE", | |
| "READ_GROUP" | |
| ] | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/MINIMUM_BASE_QUALITY", | |
| "type": "int", | |
| "default": 20, | |
| "inputBinding": { | |
| "prefix": "MINIMUM_BASE_QUALITY=", | |
| "position": 16, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/MINIMUM_MAPPING_QUALITY", | |
| "type": "int", | |
| "default": 20, | |
| "inputBinding": { | |
| "prefix": "MINIMUM_MAPPING_QUALITY=", | |
| "position": 17, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/NEAR_DISTANCE", | |
| "type": "int", | |
| "default": 250, | |
| "inputBinding": { | |
| "prefix": "NEAR_DISTANCE=", | |
| "position": 18, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/OUTPUT", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "OUTPUT=", | |
| "position": 19, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/PER_BASE_COVERAGE", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "PER_BASE_COVERAGE=", | |
| "position": 20, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/PER_TARGET_COVERAGE", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "inputBinding": { | |
| "prefix": "PER_TARGET_COVERAGE=", | |
| "position": 21, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/REFERENCE_SEQUENCE", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "REFERENCE_SEQUENCE=", | |
| "position": 22, | |
| "separate": false | |
| }, | |
| "secondaryFiles": [ | |
| ".fai" | |
| ] | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/SAMPLE_SIZE", | |
| "type": "int", | |
| "default": 10000, | |
| "inputBinding": { | |
| "prefix": "SAMPLE_SIZE=", | |
| "position": 23, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/TARGET_INTERVALS", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "TARGET_INTERVALS=", | |
| "position": 24, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/VALIDATION_STRINGENCY", | |
| "default": "STRICT", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "VALIDATION_STRINGENCY=", | |
| "position": 25, | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/java_xmx", | |
| "default": "48G", | |
| "type": "string", | |
| "inputBinding": { | |
| "position": -10, | |
| "prefix": "-Xmx", | |
| "separate": false | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#picard_collecthsmetrics.cwl/METRIC_OUTPUT", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.OUTPUT)" | |
| } | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "-jar", | |
| "position": -9 | |
| }, | |
| { | |
| "valueFrom": "/usr/local/bin/picard.jar", | |
| "position": -8 | |
| }, | |
| { | |
| "valueFrom": "CollectHsMetrics", | |
| "position": -7 | |
| } | |
| ], | |
| "baseCommand": [ | |
| "java" | |
| ], | |
| "id": "#picard_collecthsmetrics.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/picard_metrics_sqlite:e71798322233d02d67db0158aeeef27990d2d400aadfc92c3687ba85555b0cf8" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 1000, | |
| "ramMax": 1000, | |
| "tmpdirMin": 10, | |
| "tmpdirMax": 10, | |
| "outdirMin": 10, | |
| "outdirMax": 10 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/bam", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "--bam" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/input_state", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "--input_state" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/metric_path", | |
| "type": "File", | |
| "inputBinding": { | |
| "prefix": "--metric_path" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/job_uuid", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "--job_uuid" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/log", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.job_uuid+\"_picard_CollectHsMetrics.log\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl/sqlite", | |
| "format": "#picard_collecthsmetrics_to_sqlite.cwl/format_3621", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.job_uuid + \".db\")" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "/usr/local/bin/picard_metrics_sqlite", | |
| "--metric_name", | |
| "CollectHsMetrics" | |
| ], | |
| "id": "#picard_collecthsmetrics_to_sqlite.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/picard:092d034713aff237cf07ef28c22a46a113d1a59dc7ec6d71beb72295044a46f8" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 10000, | |
| "ramMax": 10000, | |
| "tmpdirMin": 10, | |
| "tmpdirMax": 10, | |
| "outdirMin": 10, | |
| "outdirMax": 10 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/DB_SNP", | |
| "type": "File", | |
| "format": "#picard_collectmultiplemetrics.cwl/format_3016", | |
| "inputBinding": { | |
| "prefix": "DB_SNP=", | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/INPUT", | |
| "type": "File", | |
| "format": "#picard_collectmultiplemetrics.cwl/format_2572", | |
| "inputBinding": { | |
| "prefix": "INPUT=", | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/METRIC_ACCUMULATION_LEVEL", | |
| "type": { | |
| "type": "array", | |
| "items": "string", | |
| "inputBinding": { | |
| "prefix": "METRIC_ACCUMULATION_LEVEL=", | |
| "separate": false | |
| } | |
| }, | |
| "default": [ | |
| "ALL_READS", | |
| "LIBRARY", | |
| "SAMPLE", | |
| "READ_GROUP" | |
| ] | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/REFERENCE_SEQUENCE", | |
| "type": "File", | |
| "format": "#picard_collectmultiplemetrics.cwl/format_1929", | |
| "inputBinding": { | |
| "prefix": "REFERENCE_SEQUENCE=", | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/TMP_DIR", | |
| "type": "string", | |
| "default": ".", | |
| "inputBinding": { | |
| "prefix": "TMP_DIR=", | |
| "separate": false | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/VALIDATION_STRINGENCY", | |
| "default": "STRICT", | |
| "type": "string", | |
| "inputBinding": { | |
| "prefix": "VALIDATION_STRINGENCY=", | |
| "separate": false | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/alignment_summary_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".alignment_summary_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/bait_bias_detail_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".bait_bias_detail_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/bait_bias_summary_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".bait_bias_summary_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/base_distribution_by_cycle_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".base_distribution_by_cycle_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/base_distribution_by_cycle_pdf", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".base_distribution_by_cycle.pdf\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/gc_bias_detail_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".gc_bias.detail_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/gc_bias_pdf", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".gc_bias.pdf\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/gc_bias_summary_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".gc_bias.summary_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/insert_size_histogram_pdf", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".insert_size_histogram.pdf\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/insert_size_metrics", | |
| "type": [ | |
| "null", | |
| "File" | |
| ], | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".insert_size_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/pre_adapter_detail_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".pre_adapter_detail_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/pre_adapter_summary_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".pre_adapter_summary_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/quality_by_cycle_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".quality_by_cycle_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/quality_by_cycle_pdf", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".quality_by_cycle.pdf\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/quality_distribution_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".quality_distribution_metrics\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/quality_distribution_pdf", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".quality_distribution.pdf\")" | |
| } | |
| }, | |
| { | |
| "id": "#picard_collectmultiplemetrics.cwl/quality_yield_metrics", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.INPUT.nameroot + \".quality_yield_metrics\")" | |
| } | |
| } | |
| ], | |
| "arguments": [ | |
| { | |
| "valueFrom": "PROGRAM=CollectAlignmentSummaryMetrics" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=CollectBaseDistributionByCycle" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=CollectGcBiasMetrics" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=CollectInsertSizeMetrics" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=CollectQualityYieldMetrics" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=CollectSequencingArtifactMetrics" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=MeanQualityByCycle" | |
| }, | |
| { | |
| "valueFrom": "PROGRAM=QualityScoreDistribution" | |
| }, | |
| { | |
| "valueFrom": "$(inputs.INPUT.nameroot)", | |
| "prefix": "OUTPUT=", | |
| "separate": false | |
| } | |
| ], | |
| "baseCommand": [ | |
| "java", | |
| "-jar", | |
| "/usr/local/bin/picard.jar", | |
| "CollectMultipleMetrics" | |
| ], | |
| "id": "#picard_collectmultiplemetrics.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/ncigdc/picard_metrics_sqlite:e71798322233d02d67db0158aeeef27990d2d400aadfc92c3687ba85555b0cf8" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 1000, | |
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| { | |
| "id": "#picard_collectwgsmetrics.cwl/OUTPUT", | |
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| { | |
| "class": "DockerRequirement", | |
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| "prefix": "--bam" | |
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| } | |
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| { | |
| "id": "#picard_collectwgsmetrics_to_sqlite.cwl/metric_path", | |
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| { | |
| "id": "#picard_collectwgsmetrics_to_sqlite.cwl/log", | |
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| "glob": "$(inputs.job_uuid+\"_picard_CollectWgsMetrics.log\")" | |
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| "prefix": "VALIDATION_STRINGENCY=", | |
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| "valueFrom": "${\n var cmd = [\"java\", \"-jar\", \"/usr/local/bin/picard.jar\", \"MergeSamFiles\"];\n var input_array = [];\n for (var i = 0; i < inputs.INPUT.length; i++) {\n for (var j = 0; j < inputs.INPUT[i].length; j++) {\n var filesize = inputs.INPUT[i][j].size;\n if (filesize > 0) {\n input_array.push(\"INPUT=\" + inputs.INPUT[i][j].path);\n }\n }\n }\n\n if (input_array.length == 0) {\n var cmd = ['/usr/bin/touch', inputs.OUTPUT];\n return cmd;\n }\n else {\n var run_cmd = cmd.concat(input_array);\n return run_cmd;\n }\n}\n" | |
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| { | |
| "id": "#picard_validatesamfile.cwl/IGNORE_WARNINGS", | |
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| "prefix": "INPUT=", | |
| "separate": false | |
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| "separate": false | |
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| { | |
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| "prefix": "MODE=", | |
| "separate": false | |
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| { | |
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| "id": "#picard_validatesamfile.cwl/OUTPUT", | |
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| 3 | |
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| { | |
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| { | |
| "id": "#picard_validatesamfile_to_sqlite.cwl/bam", | |
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| { | |
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| "prefix": "--metric_path" | |
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| "id": "#picard_validatesamfile_to_sqlite.cwl/job_uuid", | |
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| { | |
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| "requirements": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "ubuntu:bionic-20180426" | |
| }, | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "coresMin": 1, | |
| "coresMax": 1, | |
| "ramMin": 250, | |
| "ramMax": 250, | |
| "tmpdirMin": 1, | |
| "tmpdirMax": 1, | |
| "outdirMin": 1, | |
| "outdirMax": 1 | |
| } | |
| ], | |
| "class": "CommandLineTool", | |
| "inputs": [ | |
| { | |
| "id": "#touch.cwl/input", | |
| "type": "string", | |
| "inputBinding": { | |
| "position": 0 | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#touch.cwl/output", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.input)" | |
| } | |
| } | |
| ], | |
| "baseCommand": [ | |
| "touch" | |
| ], | |
| "id": "#touch.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/amplicon_kit_set_file", | |
| "type": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/fasta", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/input_state", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics", | |
| "run": "#picard_collecttargetedpcrmetrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/AMPLICON_INTERVALS", | |
| "source": "#amplicon_metrics.cwl/amplicon_kit_set_file", | |
| "valueFrom": "$(self.amplicon_kit_amplicon_file)" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/INPUT", | |
| "source": "#amplicon_metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/OUTPUT", | |
| "source": "#amplicon_metrics.cwl/bam", | |
| "valueFrom": "$(self.basename).pcrmetrics" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/REFERENCE_SEQUENCE", | |
| "source": "#amplicon_metrics.cwl/fasta" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/TARGET_INTERVALS", | |
| "source": "#amplicon_metrics.cwl/amplicon_kit_set_file", | |
| "valueFrom": "$(self.amplicon_kit_target_file)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/METRIC_OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite", | |
| "run": "#picard_collecttargetedpcrmetrics_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/bam", | |
| "source": "#amplicon_metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/input_state", | |
| "source": "#amplicon_metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/metric_path", | |
| "source": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics/METRIC_OUTPUT" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/job_uuid", | |
| "source": "#amplicon_metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/log" | |
| }, | |
| { | |
| "id": "#amplicon_metrics.cwl/picard_collecttargetedpcrmetrics_to_sqlite/sqlite" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#amplicon_metrics.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#bwa_pe.cwl/job_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/reference_sequence", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#bwa_pe.cwl/bam", | |
| "type": "File", | |
| "outputSource": "#bwa_pe.cwl/bwa_pe/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#bwa_pe.cwl/merge_sqlite/destination_sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc1", | |
| "run": "#fastqc.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc1/INPUT", | |
| "source": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "valueFrom": "$(self.forward_fastq)" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc1/threads", | |
| "source": "#bwa_pe.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc1/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc2", | |
| "run": "#fastqc.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc2/INPUT", | |
| "source": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "valueFrom": "$(self.reverse_fastq)" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc2/threads", | |
| "source": "#bwa_pe.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc2/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db1", | |
| "run": "#fastqc_db.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db1/INPUT", | |
| "source": "#bwa_pe.cwl/fastqc1/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db1/job_uuid", | |
| "source": "#bwa_pe.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db1/LOG" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db1/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db2", | |
| "run": "#fastqc_db.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db2/INPUT", | |
| "source": "#bwa_pe.cwl/fastqc2/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db2/job_uuid", | |
| "source": "#bwa_pe.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db2/LOG" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_db2/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_basicstats_json", | |
| "run": "#fastqc_basicstatistics_json.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_basicstats_json/sqlite_path", | |
| "source": "#bwa_pe.cwl/fastqc_db1/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/fastqc_basicstats_json/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe", | |
| "run": "#bwa_record_pe.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/fasta", | |
| "source": "#bwa_pe.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/fastq1", | |
| "source": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "valueFrom": "$(self.forward_fastq)" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/fastq2", | |
| "source": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "valueFrom": "$(self.reverse_fastq)" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/fastqc_json_path", | |
| "source": "#bwa_pe.cwl/fastqc_basicstats_json/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/readgroup_meta", | |
| "source": "#bwa_pe.cwl/readgroup_fastq_pe", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/thread_count", | |
| "source": "#bwa_pe.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/bwa_pe/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bam_readgroup_to_json", | |
| "run": "#bam_readgroup_to_json.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/bam_readgroup_to_json/INPUT", | |
| "source": "#bwa_pe.cwl/bwa_pe/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/bam_readgroup_to_json/MODE", | |
| "valueFrom": "lenient" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_json_db", | |
| "run": "#readgroup_json_db.cwl", | |
| "scatter": "#bwa_pe.cwl/readgroup_json_db/json_path", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_json_db/json_path", | |
| "source": "#bwa_pe.cwl/bam_readgroup_to_json/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_json_db/job_uuid", | |
| "source": "#bwa_pe.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_json_db/log" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/readgroup_json_db/output_sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/merge_readgroup_json_db", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/merge_readgroup_json_db/source_sqlite", | |
| "source": "#bwa_pe.cwl/readgroup_json_db/output_sqlite" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/merge_readgroup_json_db/job_uuid", | |
| "source": "#bwa_pe.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/merge_readgroup_json_db/destination_sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/merge_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_pe.cwl/merge_sqlite/source_sqlite", | |
| "source": [ | |
| "#bwa_pe.cwl/fastqc_db1/OUTPUT", | |
| "#bwa_pe.cwl/fastqc_db2/OUTPUT", | |
| "#bwa_pe.cwl/merge_readgroup_json_db/destination_sqlite" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/merge_sqlite/job_uuid", | |
| "source": "#bwa_pe.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_pe.cwl/merge_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#bwa_pe.cwl/merge_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#bwa_pe.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#bwa_se.cwl/job_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/reference_sequence", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/readgroup_fastq_se", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#bwa_se.cwl/bam", | |
| "type": "File", | |
| "outputSource": "#bwa_se.cwl/bwa_se/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#bwa_se.cwl/merge_sqlite/destination_sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc", | |
| "run": "#fastqc.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc/INPUT", | |
| "source": "#bwa_se.cwl/readgroup_fastq_se", | |
| "valueFrom": "$(self.fastq)" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/fastqc/threads", | |
| "source": "#bwa_se.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/fastqc_db", | |
| "run": "#fastqc_db.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc_db/INPUT", | |
| "source": "#bwa_se.cwl/fastqc/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/fastqc_db/job_uuid", | |
| "source": "#bwa_se.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc_db/LOG" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/fastqc_db/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/fastqc_basicstats_json", | |
| "run": "#fastqc_basicstatistics_json.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc_basicstats_json/sqlite_path", | |
| "source": "#bwa_se.cwl/fastqc_db/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/fastqc_basicstats_json/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bwa_se", | |
| "run": "#bwa_record_se.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/fasta", | |
| "source": "#bwa_se.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/fastq", | |
| "source": "#bwa_se.cwl/readgroup_fastq_se", | |
| "valueFrom": "$(self.fastq)" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/fastqc_json_path", | |
| "source": "#bwa_se.cwl/fastqc_basicstats_json/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/readgroup_meta", | |
| "source": "#bwa_se.cwl/readgroup_fastq_se", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/thread_count", | |
| "source": "#bwa_se.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/bwa_se/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bam_readgroup_to_json", | |
| "run": "#bam_readgroup_to_json.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/bam_readgroup_to_json/INPUT", | |
| "source": "#bwa_se.cwl/bwa_se/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/bam_readgroup_to_json/MODE", | |
| "valueFrom": "lenient" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/readgroup_json_db", | |
| "run": "#readgroup_json_db.cwl", | |
| "scatter": "#bwa_se.cwl/readgroup_json_db/json_path", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/readgroup_json_db/json_path", | |
| "source": "#bwa_se.cwl/bam_readgroup_to_json/OUTPUT" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/readgroup_json_db/job_uuid", | |
| "source": "#bwa_se.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/readgroup_json_db/log" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/readgroup_json_db/output_sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/merge_readgroup_json_db", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/merge_readgroup_json_db/source_sqlite", | |
| "source": "#bwa_se.cwl/readgroup_json_db/output_sqlite" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/merge_readgroup_json_db/job_uuid", | |
| "source": "#bwa_se.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/merge_readgroup_json_db/destination_sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/merge_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#bwa_se.cwl/merge_sqlite/source_sqlite", | |
| "source": [ | |
| "#bwa_se.cwl/fastqc_db/OUTPUT", | |
| "#bwa_se.cwl/merge_readgroup_json_db/destination_sqlite" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/merge_sqlite/job_uuid", | |
| "source": "#bwa_se.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#bwa_se.cwl/merge_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#bwa_se.cwl/merge_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#bwa_se.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/output", | |
| "type": "File", | |
| "outputSource": "#conditional_bamindex.cwl/samtools_index/output" | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#conditional_bamindex.cwl/format_sqlite/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/samtools_index", | |
| "run": "#samtools_index.cwl", | |
| "in": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/samtools_index/input", | |
| "source": "#conditional_bamindex.cwl/bam" | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/samtools_index/thread_count", | |
| "source": "#conditional_bamindex.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/samtools_index/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/empty_sqlite", | |
| "run": "#touch.cwl", | |
| "in": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/empty_sqlite/input", | |
| "valueFrom": "empty.sqlite" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/empty_sqlite/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/format_sqlite", | |
| "run": "#emit_file_format.cwl", | |
| "in": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/format_sqlite/input", | |
| "source": "#conditional_bamindex.cwl/empty_sqlite/output" | |
| }, | |
| { | |
| "id": "#conditional_bamindex.cwl/format_sqlite/format", | |
| "valueFrom": "edam:format_2572" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#conditional_bamindex.cwl/format_sqlite/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#conditional_bamindex.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/output", | |
| "type": "File", | |
| "outputSource": "#conditional_markduplicates.cwl/picard_markduplicates/OUTPUT" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates", | |
| "run": "#picard_markduplicates.cwl", | |
| "in": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates/INPUT", | |
| "source": "#conditional_markduplicates.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates/OUTPUT" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates/METRICS" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite", | |
| "run": "#picard_markduplicates_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/bam", | |
| "source": "#conditional_markduplicates.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/input_state", | |
| "valueFrom": "markduplicates_readgroups" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/metric_path", | |
| "source": "#conditional_markduplicates.cwl/picard_markduplicates/METRICS" | |
| }, | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/job_uuid", | |
| "source": "#conditional_markduplicates.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#conditional_markduplicates.cwl/picard_markduplicates_to_sqlite/sqlite" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#conditional_markduplicates.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#main/bam_name", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/bioclient_config", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#main/bioclient_load_bucket", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/job_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/amplicon_kit_set_uuid_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| } | |
| }, | |
| { | |
| "id": "#main/capture_kit_set_uuid_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#capture_kit.yml/capture_kit_set_uuid" | |
| } | |
| }, | |
| { | |
| "id": "#main/readgroup_fastq_pe_uuid_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| } | |
| }, | |
| { | |
| "id": "#main/readgroup_fastq_se_uuid_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| } | |
| }, | |
| { | |
| "id": "#main/readgroups_bam_uuid_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| }, | |
| { | |
| "id": "#main/start_token", | |
| "type": [ | |
| "null", | |
| "File" | |
| ] | |
| }, | |
| { | |
| "id": "#main/common_biallelic_vcf_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/common_biallelic_vcf_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/common_biallelic_vcf_index_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/common_biallelic_vcf_index_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/known_snp_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/known_snp_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/known_snp_index_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/known_snp_index_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_amb_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_amb_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_ann_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_ann_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_bwt_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_bwt_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_dict_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_dict_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_fa_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_fa_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_fai_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_fai_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_pac_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_pac_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/reference_sa_gdc_id", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#main/reference_sa_file_size", | |
| "type": "long" | |
| }, | |
| { | |
| "id": "#main/run_bamindex", | |
| "type": { | |
| "type": "array", | |
| "items": "long" | |
| } | |
| }, | |
| { | |
| "id": "#main/run_markduplicates", | |
| "type": { | |
| "type": "array", | |
| "items": "long" | |
| } | |
| }, | |
| { | |
| "id": "#main/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#main/indexd_bam_uuid", | |
| "type": "string", | |
| "outputSource": "#main/emit_bam_uuid/output" | |
| }, | |
| { | |
| "id": "#main/indexd_bai_uuid", | |
| "type": "string", | |
| "outputSource": "#main/emit_bai_uuid/output" | |
| }, | |
| { | |
| "id": "#main/indexd_sqlite_uuid", | |
| "type": "string", | |
| "outputSource": "#main/emit_sqlite_uuid/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#main/extract_readgroup_fastq_pe", | |
| "run": "#extract_readgroup_fastq_pe.cwl", | |
| "scatter": "#main/extract_readgroup_fastq_pe/readgroup_fastq_pe_uuid", | |
| "in": [ | |
| { | |
| "id": "#main/extract_readgroup_fastq_pe/readgroup_fastq_pe_uuid", | |
| "source": "#main/readgroup_fastq_pe_uuid_list" | |
| }, | |
| { | |
| "id": "#main/extract_readgroup_fastq_pe/bioclient_config", | |
| "source": "#main/bioclient_config" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_readgroup_fastq_pe/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_readgroup_fastq_se", | |
| "run": "#extract_readgroup_fastq_se.cwl", | |
| "scatter": "#main/extract_readgroup_fastq_se/readgroup_fastq_se_uuid", | |
| "in": [ | |
| { | |
| "id": "#main/extract_readgroup_fastq_se/readgroup_fastq_se_uuid", | |
| "source": "#main/readgroup_fastq_se_uuid_list" | |
| }, | |
| { | |
| "id": "#main/extract_readgroup_fastq_se/bioclient_config", | |
| "source": "#main/bioclient_config" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_readgroup_fastq_se/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_readgroups_bam", | |
| "run": "#extract_readgroups_bam.cwl", | |
| "scatter": [ | |
| "#main/extract_readgroups_bam/readgroups_bam_uuid" | |
| ], | |
| "in": [ | |
| { | |
| "id": "#main/extract_readgroups_bam/readgroups_bam_uuid", | |
| "source": "#main/readgroups_bam_uuid_list" | |
| }, | |
| { | |
| "id": "#main/extract_readgroups_bam/bioclient_config", | |
| "source": "#main/bioclient_config" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_readgroups_bam/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_amplicon_kits", | |
| "run": "#extract_amplicon_kit.cwl", | |
| "scatter": "#main/extract_amplicon_kits/amplicon_kit_set_uuid", | |
| "in": [ | |
| { | |
| "id": "#main/extract_amplicon_kits/bioclient_config", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_amplicon_kits/amplicon_kit_set_uuid", | |
| "source": "#main/amplicon_kit_set_uuid_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_amplicon_kits/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_capture_kits", | |
| "run": "#extract_capture_kit.cwl", | |
| "scatter": "#main/extract_capture_kits/capture_kit_set_uuid", | |
| "in": [ | |
| { | |
| "id": "#main/extract_capture_kits/bioclient_config", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_capture_kits/capture_kit_set_uuid", | |
| "source": "#main/capture_kit_set_uuid_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_capture_kits/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_common_biallelic_vcf/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf/download_handle", | |
| "source": "#main/common_biallelic_vcf_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf/file_size", | |
| "source": "#main/common_biallelic_vcf_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_common_biallelic_vcf/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf_index", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_common_biallelic_vcf_index/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf_index/download_handle", | |
| "source": "#main/common_biallelic_vcf_index_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_common_biallelic_vcf_index/file_size", | |
| "source": "#main/common_biallelic_vcf_index_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_common_biallelic_vcf_index/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_known_snp", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_known_snp/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_known_snp/download_handle", | |
| "source": "#main/known_snp_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_known_snp/file_size", | |
| "source": "#main/known_snp_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_known_snp/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_known_snp_index", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_known_snp_index/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_known_snp_index/download_handle", | |
| "source": "#main/known_snp_index_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_known_snp_index/file_size", | |
| "source": "#main/known_snp_index_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_known_snp_index/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_amb", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_amb/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_amb/download_handle", | |
| "source": "#main/reference_amb_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_amb/file_size", | |
| "source": "#main/reference_amb_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_amb/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_ann", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_ann/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_ann/download_handle", | |
| "source": "#main/reference_ann_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_ann/file_size", | |
| "source": "#main/reference_ann_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_ann/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_bwt", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_bwt/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_bwt/download_handle", | |
| "source": "#main/reference_bwt_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_bwt/file_size", | |
| "source": "#main/reference_bwt_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_bwt/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_dict", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_dict/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_dict/download_handle", | |
| "source": "#main/reference_dict_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_dict/file_size", | |
| "source": "#main/reference_dict_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_dict/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_fa", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_fa/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_fa/download_handle", | |
| "source": "#main/reference_fa_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_fa/file_size", | |
| "source": "#main/reference_fa_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_fa/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_fai", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_fai/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_fai/download_handle", | |
| "source": "#main/reference_fai_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_fai/file_size", | |
| "source": "#main/reference_fai_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_fai/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_pac", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_pac/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_pac/download_handle", | |
| "source": "#main/reference_pac_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_pac/file_size", | |
| "source": "#main/reference_pac_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_pac/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/extract_reference_sa", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/extract_reference_sa/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/extract_reference_sa/download_handle", | |
| "source": "#main/reference_sa_gdc_id" | |
| }, | |
| { | |
| "id": "#main/extract_reference_sa/file_size", | |
| "source": "#main/reference_sa_file_size" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/extract_reference_sa/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/root_fasta_files", | |
| "run": "#root_fasta_dnaseq.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/root_fasta_files/fasta", | |
| "source": "#main/extract_reference_fa/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_amb", | |
| "source": "#main/extract_reference_amb/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_ann", | |
| "source": "#main/extract_reference_ann/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_bwt", | |
| "source": "#main/extract_reference_bwt/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_dict", | |
| "source": "#main/extract_reference_dict/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_fai", | |
| "source": "#main/extract_reference_fai/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_pac", | |
| "source": "#main/extract_reference_pac/output" | |
| }, | |
| { | |
| "id": "#main/root_fasta_files/fasta_sa", | |
| "source": "#main/extract_reference_sa/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/root_fasta_files/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/root_common_biallelic_vcf_files", | |
| "run": "#root_vcf.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/root_common_biallelic_vcf_files/vcf", | |
| "source": "#main/extract_common_biallelic_vcf/output" | |
| }, | |
| { | |
| "id": "#main/root_common_biallelic_vcf_files/vcf_index", | |
| "source": "#main/extract_common_biallelic_vcf_index/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/root_common_biallelic_vcf_files/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/root_known_snp_files", | |
| "run": "#root_vcf.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/root_known_snp_files/vcf", | |
| "source": "#main/extract_known_snp/output" | |
| }, | |
| { | |
| "id": "#main/root_known_snp_files/vcf_index", | |
| "source": "#main/extract_known_snp_index/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/root_known_snp_files/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/transform", | |
| "run": "#transform.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/transform/bam_name", | |
| "source": "#main/bam_name" | |
| }, | |
| { | |
| "id": "#main/transform/job_uuid", | |
| "source": "#main/job_uuid" | |
| }, | |
| { | |
| "id": "#main/transform/amplicon_kit_set_file_list", | |
| "source": "#main/extract_amplicon_kits/output" | |
| }, | |
| { | |
| "id": "#main/transform/capture_kit_set_file_list", | |
| "source": "#main/extract_capture_kits/output" | |
| }, | |
| { | |
| "id": "#main/transform/readgroup_fastq_pe_file_list", | |
| "source": "#main/extract_readgroup_fastq_pe/output" | |
| }, | |
| { | |
| "id": "#main/transform/readgroup_fastq_se_file_list", | |
| "source": "#main/extract_readgroup_fastq_se/output" | |
| }, | |
| { | |
| "id": "#main/transform/readgroups_bam_file_list", | |
| "source": "#main/extract_readgroups_bam/output" | |
| }, | |
| { | |
| "id": "#main/transform/common_biallelic_vcf", | |
| "source": "#main/root_common_biallelic_vcf_files/output" | |
| }, | |
| { | |
| "id": "#main/transform/known_snp", | |
| "source": "#main/root_known_snp_files/output" | |
| }, | |
| { | |
| "id": "#main/transform/reference_sequence", | |
| "source": "#main/root_fasta_files/output" | |
| }, | |
| { | |
| "id": "#main/transform/run_bamindex", | |
| "source": "#main/run_bamindex" | |
| }, | |
| { | |
| "id": "#main/transform/run_markduplicates", | |
| "source": "#main/run_markduplicates" | |
| }, | |
| { | |
| "id": "#main/transform/thread_count", | |
| "source": "#main/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/transform/output_bam" | |
| }, | |
| { | |
| "id": "#main/transform/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/load_bam", | |
| "run": "#bio_client_upload_pull_uuid.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/load_bam/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/load_bam/input", | |
| "source": "#main/transform/output_bam" | |
| }, | |
| { | |
| "id": "#main/load_bam/upload-bucket", | |
| "source": "#main/bioclient_load_bucket" | |
| }, | |
| { | |
| "id": "#main/load_bam/upload-key", | |
| "valueFrom": "$(inputs.job_uuid)/$(inputs.input.basename)" | |
| }, | |
| { | |
| "id": "#main/load_bam/job_uuid", | |
| "source": "#main/job_uuid", | |
| "valueFrom": "$(null)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/load_bam/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/load_bai", | |
| "run": "#bio_client_upload_pull_uuid.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/load_bai/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/load_bai/input", | |
| "source": "#main/transform/output_bam", | |
| "valueFrom": "$(self.secondaryFiles[0])" | |
| }, | |
| { | |
| "id": "#main/load_bai/upload-bucket", | |
| "source": "#main/bioclient_load_bucket" | |
| }, | |
| { | |
| "id": "#main/load_bai/upload-key", | |
| "valueFrom": "$(inputs.job_uuid)/$(inputs.input.nameroot).bai" | |
| }, | |
| { | |
| "id": "#main/load_bai/job_uuid", | |
| "source": "#main/job_uuid", | |
| "valueFrom": "$(null)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/load_bai/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/load_sqlite", | |
| "run": "#bio_client_upload_pull_uuid.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/load_sqlite/config-file", | |
| "source": "#main/bioclient_config" | |
| }, | |
| { | |
| "id": "#main/load_sqlite/input", | |
| "source": "#main/transform/sqlite" | |
| }, | |
| { | |
| "id": "#main/load_sqlite/upload-bucket", | |
| "source": "#main/bioclient_load_bucket" | |
| }, | |
| { | |
| "id": "#main/load_sqlite/upload-key", | |
| "valueFrom": "$(inputs.job_uuid)/$(inputs.input.basename)" | |
| }, | |
| { | |
| "id": "#main/load_sqlite/job_uuid", | |
| "source": "#main/job_uuid", | |
| "valueFrom": "$(null)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/load_sqlite/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/emit_bam_uuid", | |
| "run": "#emit_json_value.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/emit_bam_uuid/input", | |
| "source": "#main/load_bam/output" | |
| }, | |
| { | |
| "id": "#main/emit_bam_uuid/key", | |
| "valueFrom": "did" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/emit_bam_uuid/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/emit_bai_uuid", | |
| "run": "#emit_json_value.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/emit_bai_uuid/input", | |
| "source": "#main/load_bai/output" | |
| }, | |
| { | |
| "id": "#main/emit_bai_uuid/key", | |
| "valueFrom": "did" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/emit_bai_uuid/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#main/emit_sqlite_uuid", | |
| "run": "#emit_json_value.cwl", | |
| "in": [ | |
| { | |
| "id": "#main/emit_sqlite_uuid/input", | |
| "source": "#main/load_sqlite/output" | |
| }, | |
| { | |
| "id": "#main/emit_sqlite_uuid/key", | |
| "valueFrom": "did" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/emit_sqlite_uuid/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#main" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#exome_metrics.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/capture_kit_set_file", | |
| "type": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/fasta", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/input_state", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#exome_metrics.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics", | |
| "run": "#picard_collecthsmetrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/BAIT_INTERVALS", | |
| "source": "#exome_metrics.cwl/capture_kit_set_file", | |
| "valueFrom": "$(self.capture_kit_bait_file)" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/INPUT", | |
| "source": "#exome_metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/OUTPUT", | |
| "source": "#exome_metrics.cwl/bam", | |
| "valueFrom": "$(self.basename).hsmetrics" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/REFERENCE_SEQUENCE", | |
| "source": "#exome_metrics.cwl/fasta" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/TARGET_INTERVALS", | |
| "source": "#exome_metrics.cwl/capture_kit_set_file", | |
| "valueFrom": "$(self.capture_kit_target_file)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics/METRIC_OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite", | |
| "run": "#picard_collecthsmetrics_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/bam", | |
| "source": "#exome_metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/input_state", | |
| "source": "#exome_metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/metric_path", | |
| "source": "#exome_metrics.cwl/picard_collecthsmetrics/METRIC_OUTPUT" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/job_uuid", | |
| "source": "#exome_metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/log" | |
| }, | |
| { | |
| "id": "#exome_metrics.cwl/picard_collecthsmetrics_to_sqlite/sqlite" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#exome_metrics.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/bioclient_config", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/amplicon_kit_set_uuid", | |
| "type": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/output", | |
| "type": "#amplicon_kit.yml/amplicon_kit_set_file", | |
| "outputSource": "#extract_amplicon_kit.cwl/emit_amplicon_kit/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_amplicon", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_amplicon/config-file", | |
| "source": "#extract_amplicon_kit.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_amplicon/download_handle", | |
| "source": "#extract_amplicon_kit.cwl/amplicon_kit_set_uuid", | |
| "valueFrom": "$(self.amplicon_kit_amplicon_uuid)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_amplicon/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_target", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_target/config-file", | |
| "source": "#extract_amplicon_kit.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_target/download_handle", | |
| "source": "#extract_amplicon_kit.cwl/amplicon_kit_set_uuid", | |
| "valueFrom": "$(self.amplicon_kit_target_uuid)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/extract_amplicon_kit_target/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/emit_amplicon_kit", | |
| "run": "#emit_amplicon_kit_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/emit_amplicon_kit/amplicon_kit_amplicon_file", | |
| "source": "#extract_amplicon_kit.cwl/extract_amplicon_kit_amplicon/output" | |
| }, | |
| { | |
| "id": "#extract_amplicon_kit.cwl/emit_amplicon_kit/amplicon_kit_target_file", | |
| "source": "#extract_amplicon_kit.cwl/extract_amplicon_kit_target/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_amplicon_kit.cwl/emit_amplicon_kit/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#extract_amplicon_kit.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/bioclient_config", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/capture_kit_set_uuid", | |
| "type": "#capture_kit.yml/capture_kit_set_uuid" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/output", | |
| "type": "#capture_kit.yml/capture_kit_set_file", | |
| "outputSource": "#extract_capture_kit.cwl/emit_capture_kit/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_bait", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_bait/config-file", | |
| "source": "#extract_capture_kit.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_bait/download_handle", | |
| "source": "#extract_capture_kit.cwl/capture_kit_set_uuid", | |
| "valueFrom": "$(self.capture_kit_bait_uuid)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_bait/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_target", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_target/config-file", | |
| "source": "#extract_capture_kit.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_target/download_handle", | |
| "source": "#extract_capture_kit.cwl/capture_kit_set_uuid", | |
| "valueFrom": "$(self.capture_kit_target_uuid)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/extract_capture_kit_target/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/emit_capture_kit", | |
| "run": "#emit_capture_kit_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/emit_capture_kit/capture_kit_bait_file", | |
| "source": "#extract_capture_kit.cwl/extract_capture_kit_bait/output" | |
| }, | |
| { | |
| "id": "#extract_capture_kit.cwl/emit_capture_kit/capture_kit_target_file", | |
| "source": "#extract_capture_kit.cwl/extract_capture_kit_target/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_capture_kit.cwl/emit_capture_kit/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#extract_capture_kit.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/bioclient_config", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file", | |
| "outputSource": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq/config-file", | |
| "source": "#extract_readgroup_fastq_pe.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq/download_handle", | |
| "source": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "valueFrom": "$(self.forward_fastq_uuid)" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq/file_size", | |
| "source": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "valueFrom": "$(self.forward_fastq_file_size)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq/config-file", | |
| "source": "#extract_readgroup_fastq_pe.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq/download_handle", | |
| "source": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "valueFrom": "$(self.reverse_fastq_uuid)" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq/file_size", | |
| "source": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "valueFrom": "$(self.reverse_fastq_file_size)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file", | |
| "run": "#emit_readgroup_fastq_pe_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file/forward_fastq", | |
| "source": "#extract_readgroup_fastq_pe.cwl/extract_forward_fastq/output" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file/reverse_fastq", | |
| "source": "#extract_readgroup_fastq_pe.cwl/extract_reverse_fastq/output" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file/readgroup_meta", | |
| "source": "#extract_readgroup_fastq_pe.cwl/readgroup_fastq_pe_uuid", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe_file/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#extract_readgroup_fastq_pe.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/readgroup_fastq_se_uuid", | |
| "type": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/bioclient_config", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file", | |
| "outputSource": "#extract_readgroup_fastq_se.cwl/emit_readgroup_fastq_se_file/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/extract_fastq", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/extract_fastq/config-file", | |
| "source": "#extract_readgroup_fastq_se.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/extract_fastq/download_handle", | |
| "source": "#extract_readgroup_fastq_se.cwl/readgroup_fastq_se_uuid", | |
| "valueFrom": "$(self.fastq_uuid)" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/extract_fastq/file_size", | |
| "source": "#extract_readgroup_fastq_se.cwl/readgroup_fastq_se_uuid", | |
| "valueFrom": "$(self.fastq_file_size)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/extract_fastq/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/emit_readgroup_fastq_se_file", | |
| "run": "#emit_readgroup_fastq_se_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/emit_readgroup_fastq_se_file/fastq", | |
| "source": "#extract_readgroup_fastq_se.cwl/extract_fastq/output" | |
| }, | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/emit_readgroup_fastq_se_file/readgroup_meta", | |
| "source": "#extract_readgroup_fastq_se.cwl/readgroup_fastq_se_uuid", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroup_fastq_se.cwl/emit_readgroup_fastq_se_file/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#extract_readgroup_fastq_se.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/bioclient_config", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#extract_readgroups_bam.cwl/readgroups_bam_uuid", | |
| "type": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/output", | |
| "type": "#readgroup.yml/readgroups_bam_file", | |
| "outputSource": "#extract_readgroups_bam.cwl/emit_readgroups_bam_file/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/extract_bam", | |
| "run": "#bio_client_download.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/extract_bam/config-file", | |
| "source": "#extract_readgroups_bam.cwl/bioclient_config" | |
| }, | |
| { | |
| "id": "#extract_readgroups_bam.cwl/extract_bam/download_handle", | |
| "source": "#extract_readgroups_bam.cwl/readgroups_bam_uuid", | |
| "valueFrom": "$(self.bam_uuid)" | |
| }, | |
| { | |
| "id": "#extract_readgroups_bam.cwl/extract_bam/file_size", | |
| "source": "#extract_readgroups_bam.cwl/readgroups_bam_uuid", | |
| "valueFrom": "$(self.bam_file_size)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/extract_bam/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#extract_readgroups_bam.cwl/emit_readgroups_bam_file", | |
| "run": "#emit_readgroups_bam_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/emit_readgroups_bam_file/bam", | |
| "source": "#extract_readgroups_bam.cwl/extract_bam/output" | |
| }, | |
| { | |
| "id": "#extract_readgroups_bam.cwl/emit_readgroups_bam_file/readgroup_meta_list", | |
| "source": "#extract_readgroups_bam.cwl/readgroups_bam_uuid", | |
| "valueFrom": "$(self.readgroup_meta_list)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#extract_readgroups_bam.cwl/emit_readgroups_bam_file/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#extract_readgroups_bam.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "Workflow", | |
| "inputs": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/input", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file", | |
| "outputSource": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file/output" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#fastq_clean_pe.cwl/json_to_sqlite/sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe", | |
| "run": "#fastq_cleaner_pe.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe/fastq1", | |
| "source": "#fastq_clean_pe.cwl/input", | |
| "valueFrom": "$(self.forward_fastq)" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe/fastq2", | |
| "source": "#fastq_clean_pe.cwl/input", | |
| "valueFrom": "$(self.reverse_fastq)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe/cleaned_fastq1" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe/cleaned_fastq2" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/fastq_cleaner_pe/result_json" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file", | |
| "run": "#emit_readgroup_fastq_pe_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file/forward_fastq", | |
| "source": "#fastq_clean_pe.cwl/fastq_cleaner_pe/cleaned_fastq1" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file/reverse_fastq", | |
| "source": "#fastq_clean_pe.cwl/fastq_cleaner_pe/cleaned_fastq2" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file/readgroup_meta", | |
| "source": "#fastq_clean_pe.cwl/input", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/emit_readgroup_fastq_pe_file/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite", | |
| "run": "#json_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite/input_json", | |
| "source": "#fastq_clean_pe.cwl/fastq_cleaner_pe/result_json" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite/job_uuid", | |
| "source": "#fastq_clean_pe.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite/table_name", | |
| "valueFrom": "fastq_cleaner_pe" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite/sqlite" | |
| }, | |
| { | |
| "id": "#fastq_clean_pe.cwl/json_to_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#fastq_clean_pe.cwl" | |
| }, | |
| { | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "class": "Workflow", | |
| "inputs": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/input", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file", | |
| "outputSource": "#fastq_clean_se.cwl/emit_readgroup_fastq_se_file/output" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#fastq_clean_se.cwl/json_to_sqlite/sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/fastq_cleaner_se", | |
| "run": "#fastq_cleaner_se.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/fastq_cleaner_se/fastq", | |
| "source": "#fastq_clean_se.cwl/input", | |
| "valueFrom": "$(self.fastq)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/fastq_cleaner_se/cleaned_fastq" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/fastq_cleaner_se/result_json" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/emit_readgroup_fastq_se_file", | |
| "run": "#emit_readgroup_fastq_se_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/emit_readgroup_fastq_se_file/fastq", | |
| "source": "#fastq_clean_se.cwl/fastq_cleaner_se/cleaned_fastq" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/emit_readgroup_fastq_se_file/readgroup_meta", | |
| "source": "#fastq_clean_se.cwl/input", | |
| "valueFrom": "$(self.readgroup_meta)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/emit_readgroup_fastq_se_file/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite", | |
| "run": "#json_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite/input_json", | |
| "source": "#fastq_clean_se.cwl/fastq_cleaner_se/result_json" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite/job_uuid", | |
| "source": "#fastq_clean_se.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite/table_name", | |
| "valueFrom": "fastq_cleaner_se" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite/sqlite" | |
| }, | |
| { | |
| "id": "#fastq_clean_se.cwl/json_to_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#fastq_clean_se.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "MultipleInputFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#integrity.cwl/bai", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#integrity.cwl/input_state", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#integrity.cwl/job_uuid", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#integrity.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#integrity.cwl/merge_sqlite/destination_sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#integrity.cwl/bai_ls_l", | |
| "run": "#ls_l.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bai_ls_l/INPUT", | |
| "source": "#integrity.cwl/bai" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bai_ls_l/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_md5sum", | |
| "run": "#md5sum.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bai_md5sum/INPUT", | |
| "source": "#integrity.cwl/bai" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bai_md5sum/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_sha256", | |
| "run": "#sha256sum.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bai_sha256/INPUT", | |
| "source": "#integrity.cwl/bai" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bai_sha256/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_ls_l", | |
| "run": "#ls_l.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bam_ls_l/INPUT", | |
| "source": "#integrity.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bam_ls_l/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_md5sum", | |
| "run": "#md5sum.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bam_md5sum/INPUT", | |
| "source": "#integrity.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bam_md5sum/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_sha256", | |
| "run": "#sha256sum.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bam_sha256/INPUT", | |
| "source": "#integrity.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bam_sha256/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db", | |
| "run": "#integrity_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/input_state", | |
| "source": "#integrity.cwl/input_state" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/ls_l_path", | |
| "source": "#integrity.cwl/bai_ls_l/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/md5sum_path", | |
| "source": "#integrity.cwl/bai_md5sum/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/sha256sum_path", | |
| "source": "#integrity.cwl/bai_sha256/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/job_uuid", | |
| "source": "#integrity.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bai_integrity_to_db/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db", | |
| "run": "#integrity_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/input_state", | |
| "source": "#integrity.cwl/input_state" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/ls_l_path", | |
| "source": "#integrity.cwl/bam_ls_l/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/md5sum_path", | |
| "source": "#integrity.cwl/bam_md5sum/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/sha256sum_path", | |
| "source": "#integrity.cwl/bam_sha256/OUTPUT" | |
| }, | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/job_uuid", | |
| "source": "#integrity.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/bam_integrity_to_db/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/merge_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#integrity.cwl/merge_sqlite/source_sqlite", | |
| "source": [ | |
| "#integrity.cwl/bai_integrity_to_db/OUTPUT", | |
| "#integrity.cwl/bam_integrity_to_db/OUTPUT" | |
| ] | |
| }, | |
| { | |
| "id": "#integrity.cwl/merge_sqlite/job_uuid", | |
| "source": "#integrity.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#integrity.cwl/merge_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#integrity.cwl/merge_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#integrity.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#metrics.cwl/bam", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| "^.bai" | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/amplicon_kit_set_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| } | |
| }, | |
| { | |
| "id": "#metrics.cwl/capture_kit_set_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#capture_kit.yml/capture_kit_set_file" | |
| } | |
| }, | |
| { | |
| "id": "#metrics.cwl/common_biallelic_vcf", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".tbi" | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/fasta", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/input_state", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#metrics.cwl/job_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#metrics.cwl/known_snp", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".tbi" | |
| ] | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#metrics.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#metrics.cwl/merge_sqlite/destination_sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics", | |
| "run": "#amplicon_metrics.cwl", | |
| "scatter": "#metrics.cwl/amplicon_metrics/amplicon_kit_set_file", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/bam", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/amplicon_kit_set_file", | |
| "source": "#metrics.cwl/amplicon_kit_set_file_list" | |
| }, | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/fasta", | |
| "source": "#metrics.cwl/fasta" | |
| }, | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/amplicon_metrics/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/exome_metrics", | |
| "run": "#exome_metrics.cwl", | |
| "scatter": "#metrics.cwl/exome_metrics/capture_kit_set_file", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/exome_metrics/bam", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/exome_metrics/capture_kit_set_file", | |
| "source": "#metrics.cwl/capture_kit_set_file_list" | |
| }, | |
| { | |
| "id": "#metrics.cwl/exome_metrics/fasta", | |
| "source": "#metrics.cwl/fasta" | |
| }, | |
| { | |
| "id": "#metrics.cwl/exome_metrics/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/exome_metrics/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/exome_metrics/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_exome_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/merge_exome_sqlite/source_sqlite", | |
| "source": "#metrics.cwl/exome_metrics/sqlite" | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_exome_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/merge_exome_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_exome_sqlite/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_amplicon_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/merge_amplicon_sqlite/source_sqlite", | |
| "source": "#metrics.cwl/amplicon_metrics/sqlite" | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_amplicon_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/merge_amplicon_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_amplicon_sqlite/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_getpileupsummaries", | |
| "run": "#gatk4_getpileupsummaries.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/gatk_getpileupsummaries/input", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_getpileupsummaries/variant", | |
| "source": "#metrics.cwl/common_biallelic_vcf" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/gatk_getpileupsummaries/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination", | |
| "run": "#gatk4_calculatecontamination.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination/input", | |
| "source": "#metrics.cwl/gatk_getpileupsummaries/output" | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination/bam_nameroot", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.nameroot)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite", | |
| "run": "#gatk_calculatecontamination_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/gatk_calculatecontamination/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/gatk_calculatecontamination_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics", | |
| "run": "#picard_collectmultiplemetrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/DB_SNP", | |
| "source": "#metrics.cwl/known_snp" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/REFERENCE_SEQUENCE", | |
| "source": "#metrics.cwl/fasta" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/alignment_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/bait_bias_detail_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/bait_bias_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/base_distribution_by_cycle_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/gc_bias_detail_metrics" | |
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| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/gc_bias_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/insert_size_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/pre_adapter_detail_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/pre_adapter_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/quality_by_cycle_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/quality_distribution_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics/quality_yield_metrics" | |
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| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite", | |
| "run": "#picard_collectmultiplemetrics_to_sqlite.cwl", | |
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| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/fasta", | |
| "source": "#metrics.cwl/fasta", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/vcf", | |
| "source": "#metrics.cwl/known_snp", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/alignment_summary_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/alignment_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/bait_bias_detail_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/bait_bias_detail_metrics" | |
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| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/bait_bias_summary_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/bait_bias_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/base_distribution_by_cycle_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/base_distribution_by_cycle_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/gc_bias_detail_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/gc_bias_detail_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/gc_bias_summary_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/gc_bias_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/insert_size_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/insert_size_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/pre_adapter_detail_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/pre_adapter_detail_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/pre_adapter_summary_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/pre_adapter_summary_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/quality_by_cycle_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/quality_by_cycle_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/quality_distribution_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/quality_distribution_metrics" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/quality_yield_metrics", | |
| "source": "#metrics.cwl/picard_collectmultiplemetrics/quality_yield_metrics" | |
| } | |
| ], | |
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| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/log" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics", | |
| "run": "#picard_collectoxogmetrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics/DB_SNP", | |
| "source": "#metrics.cwl/known_snp" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics/REFERENCE_SEQUENCE", | |
| "source": "#metrics.cwl/fasta" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite", | |
| "run": "#picard_collectoxogmetrics_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/fasta", | |
| "source": "#metrics.cwl/fasta", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/picard_collectoxogmetrics/OUTPUT" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/vcf", | |
| "source": "#metrics.cwl/known_snp", | |
| "valueFrom": "$(self.basename)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/log" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics", | |
| "run": "#picard_collectwgsmetrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics/REFERENCE_SEQUENCE", | |
| "source": "#metrics.cwl/fasta" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite", | |
| "run": "#picard_collectwgsmetrics_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/fasta", | |
| "source": "#metrics.cwl/fasta", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/picard_collectwgsmetrics/OUTPUT" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/log" | |
| }, | |
| { | |
| "id": "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat", | |
| "run": "#samtools_flagstat.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite", | |
| "run": "#samtools_flagstat_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/samtools_flagstat/OUTPUT" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_flagstat_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats", | |
| "run": "#samtools_idxstats.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite", | |
| "run": "#samtools_idxstats_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/samtools_idxstats/OUTPUT" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_idxstats_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_stats", | |
| "run": "#samtools_stats.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_stats/INPUT", | |
| "source": "#metrics.cwl/bam" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_stats/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite", | |
| "run": "#samtools_stats_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite/bam", | |
| "source": "#metrics.cwl/bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite/input_state", | |
| "source": "#metrics.cwl/input_state" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite/metric_path", | |
| "source": "#metrics.cwl/samtools_stats/OUTPUT" | |
| }, | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/samtools_stats_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#metrics.cwl/merge_sqlite/source_sqlite", | |
| "source": [ | |
| "#metrics.cwl/gatk_calculatecontamination_to_sqlite/sqlite", | |
| "#metrics.cwl/merge_exome_sqlite/destination_sqlite", | |
| "#metrics.cwl/merge_amplicon_sqlite/destination_sqlite", | |
| "#metrics.cwl/picard_collectmultiplemetrics_to_sqlite/sqlite", | |
| "#metrics.cwl/picard_collectoxogmetrics_to_sqlite/sqlite", | |
| "#metrics.cwl/picard_collectwgsmetrics_to_sqlite/sqlite", | |
| "#metrics.cwl/samtools_flagstat_to_sqlite/sqlite", | |
| "#metrics.cwl/samtools_idxstats_to_sqlite/sqlite", | |
| "#metrics.cwl/samtools_stats_to_sqlite/sqlite" | |
| ] | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_sqlite/job_uuid", | |
| "source": "#metrics.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#metrics.cwl/merge_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#metrics.cwl/merge_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#metrics.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/forward_fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/reverse_fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/readgroup_json", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_pe_file", | |
| "outputSource": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_json_readgroup_meta", | |
| "run": "#emit_json_readgroup_meta.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_json_readgroup_meta/input", | |
| "source": "#readgroup_fastq_pe.cwl/readgroup_json" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_json_readgroup_meta/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe", | |
| "run": "#emit_readgroup_fastq_pe_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe/forward_fastq", | |
| "source": "#readgroup_fastq_pe.cwl/forward_fastq" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe/reverse_fastq", | |
| "source": "#readgroup_fastq_pe.cwl/reverse_fastq" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe/readgroup_meta", | |
| "source": "#readgroup_fastq_pe.cwl/emit_json_readgroup_meta/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroup_fastq_pe.cwl/emit_readgroup_fastq_pe/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#readgroup_fastq_pe.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/fastq", | |
| "type": "File" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_se.cwl/readgroup_json", | |
| "type": "File" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/output", | |
| "type": "#readgroup.yml/readgroup_fastq_se_file", | |
| "outputSource": "#readgroup_fastq_se.cwl/emit_readgroup_fastq_se/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_json_readgroup_meta", | |
| "run": "#emit_json_readgroup_meta.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_json_readgroup_meta/input", | |
| "source": "#readgroup_fastq_se.cwl/readgroup_json" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_json_readgroup_meta/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_readgroup_fastq_se", | |
| "run": "#emit_readgroup_fastq_se_file.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_readgroup_fastq_se/fastq", | |
| "source": "#readgroup_fastq_se.cwl/fastq" | |
| }, | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_readgroup_fastq_se/readgroup_meta", | |
| "source": "#readgroup_fastq_se.cwl/emit_json_readgroup_meta/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroup_fastq_se.cwl/emit_readgroup_fastq_se/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#readgroup_fastq_se.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroups_bam_file", | |
| "type": "#readgroup.yml/readgroups_bam_file" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/pe_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| "outputSource": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/output" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/se_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| "outputSource": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/output" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/o1_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| "outputSource": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/output" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/o2_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| "outputSource": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/output" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq", | |
| "run": "#biobambam2_bamtofastq.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/filename", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroups_bam_file", | |
| "valueFrom": "$(self.bam)" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq2" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o2" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_s" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json", | |
| "run": "#bam_readgroup_to_json.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/INPUT", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroups_bam_file", | |
| "valueFrom": "$(self.bam)" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/MODE", | |
| "valueFrom": "lenient" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_pe", | |
| "run": "#decider_readgroup_expression.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_pe/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_pe/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_pe/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_se", | |
| "run": "#decider_readgroup_expression.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_se/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_s" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_se/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_se/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o1", | |
| "run": "#decider_readgroup_expression.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o1/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o1/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o1/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o2", | |
| "run": "#decider_readgroup_expression.cwl", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o2/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o2" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o2/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/bam_readgroup_to_json/OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o2/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe", | |
| "run": "#readgroup_fastq_pe.cwl", | |
| "scatter": [ | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/forward_fastq", | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/reverse_fastq", | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/readgroup_json" | |
| ], | |
| "scatterMethod": "dotproduct", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/forward_fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/reverse_fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq2" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_pe/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_pe/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se", | |
| "run": "#readgroup_fastq_se.cwl", | |
| "scatter": [ | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/fastq", | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/readgroup_json" | |
| ], | |
| "scatterMethod": "dotproduct", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_s" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_se/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_se/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1", | |
| "run": "#readgroup_fastq_se.cwl", | |
| "scatter": [ | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/fastq", | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/readgroup_json" | |
| ], | |
| "scatterMethod": "dotproduct", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o1" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o1/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o1/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2", | |
| "run": "#readgroup_fastq_se.cwl", | |
| "scatter": [ | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/fastq", | |
| "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/readgroup_json" | |
| ], | |
| "scatterMethod": "dotproduct", | |
| "in": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/fastq", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/biobambam_bamtofastq/output_fastq_o2" | |
| }, | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/readgroup_json", | |
| "source": "#readgroups_bam_to_readgroups_fastq_lists.cwl/decider_readgroup_o2/output" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl/readgroup_fastq_o2/output" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#readgroups_bam_to_readgroups_fastq_lists.cwl" | |
| }, | |
| { | |
| "class": "Workflow", | |
| "requirements": [ | |
| { | |
| "class": "InlineJavascriptRequirement" | |
| }, | |
| { | |
| "class": "MultipleInputFeatureRequirement" | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SchemaDefRequirement", | |
| "types": [ | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| }, | |
| { | |
| "$import": "#amplicon_kit.yml/amplicon_kit_set_uuid" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_file" | |
| }, | |
| { | |
| "$import": "#capture_kit.yml/capture_kit_set_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_meta" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_file" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_pe_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroup_fastq_se_uuid" | |
| }, | |
| { | |
| "$import": "#readgroup.yml/readgroups_bam_uuid" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "StepInputExpressionRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#transform.cwl/bam_name", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#transform.cwl/job_uuid", | |
| "type": "string" | |
| }, | |
| { | |
| "id": "#transform.cwl/amplicon_kit_set_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#amplicon_kit.yml/amplicon_kit_set_file" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/capture_kit_set_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#capture_kit.yml/capture_kit_set_file" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroup_fastq_pe_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_pe_file" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroup_fastq_se_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroup_fastq_se_file" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroups_bam_file_list", | |
| "type": { | |
| "type": "array", | |
| "items": "#readgroup.yml/readgroups_bam_file" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/common_biallelic_vcf", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".tbi" | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/known_snp", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".tbi" | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/run_bamindex", | |
| "type": { | |
| "type": "array", | |
| "items": "long" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/run_markduplicates", | |
| "type": { | |
| "type": "array", | |
| "items": "long" | |
| } | |
| }, | |
| { | |
| "id": "#transform.cwl/reference_sequence", | |
| "type": "File", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".fai", | |
| ".pac", | |
| ".sa", | |
| "^.dict" | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/thread_count", | |
| "type": "long" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#transform.cwl/output_bam", | |
| "type": "File", | |
| "outputSource": "#transform.cwl/gatk_applybqsr/output_bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/sqlite", | |
| "type": "File", | |
| "outputSource": "#transform.cwl/merge_all_sqlite/destination_sqlite" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#transform.cwl/fastq_clean_pe", | |
| "run": "#fastq_clean_pe.cwl", | |
| "scatter": "#transform.cwl/fastq_clean_pe/input", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/fastq_clean_pe/input", | |
| "source": "#transform.cwl/readgroup_fastq_pe_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/fastq_clean_pe/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/fastq_clean_pe/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/fastq_clean_pe/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/fastq_clean_se", | |
| "run": "#fastq_clean_se.cwl", | |
| "scatter": "#transform.cwl/fastq_clean_se/input", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/fastq_clean_se/input", | |
| "source": "#transform.cwl/readgroup_fastq_se_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/fastq_clean_se/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/fastq_clean_se/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/fastq_clean_se/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_pe", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_pe/source_sqlite", | |
| "source": "#transform.cwl/fastq_clean_pe/sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_pe/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_pe/destination_sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_pe/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_se", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_se/source_sqlite", | |
| "source": "#transform.cwl/fastq_clean_se/sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_se/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_se/destination_sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_fastq_clean_se/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists", | |
| "run": "#readgroups_bam_to_readgroups_fastq_lists.cwl", | |
| "scatter": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/readgroups_bam_file", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/readgroups_bam_file", | |
| "source": "#transform.cwl/readgroups_bam_file_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/pe_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/se_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/o1_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/o2_file_list" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_bam_pe_fastq_records", | |
| "run": "#merge_pe_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_bam_pe_fastq_records/input", | |
| "source": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/pe_file_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_bam_pe_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_pe_fastq_records", | |
| "run": "#merge_pe_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_pe_fastq_records/input", | |
| "source": [ | |
| "#transform.cwl/merge_bam_pe_fastq_records/output", | |
| "#transform.cwl/fastq_clean_pe/output" | |
| ] | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_pe_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_bam_se_fastq_records", | |
| "run": "#merge_se_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_bam_se_fastq_records/input", | |
| "source": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/se_file_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_bam_se_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_se_fastq_records", | |
| "run": "#merge_se_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_se_fastq_records/input", | |
| "source": [ | |
| "#transform.cwl/merge_bam_se_fastq_records/output", | |
| "#transform.cwl/fastq_clean_se/output" | |
| ] | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_se_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_o1_fastq_records", | |
| "run": "#merge_se_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_o1_fastq_records/input", | |
| "source": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/o1_file_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_o1_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_o2_fastq_records", | |
| "run": "#merge_se_fastq_records.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_o2_fastq_records/input", | |
| "source": "#transform.cwl/readgroups_bam_to_readgroups_fastq_lists/o2_file_list" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_o2_fastq_records/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_pe", | |
| "run": "#bwa_pe.cwl", | |
| "scatter": "#transform.cwl/bwa_pe/readgroup_fastq_pe", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/bwa_pe/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_pe/reference_sequence", | |
| "source": "#transform.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_pe/readgroup_fastq_pe", | |
| "source": "#transform.cwl/merge_pe_fastq_records/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_pe/thread_count", | |
| "source": "#transform.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/bwa_pe/bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_pe/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_se", | |
| "run": "#bwa_se.cwl", | |
| "scatter": "#transform.cwl/bwa_se/readgroup_fastq_se", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/bwa_se/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_se/reference_sequence", | |
| "source": "#transform.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_se/readgroup_fastq_se", | |
| "source": "#transform.cwl/merge_se_fastq_records/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_se/thread_count", | |
| "source": "#transform.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/bwa_se/bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_se/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o1", | |
| "run": "#bwa_se.cwl", | |
| "scatter": "#transform.cwl/bwa_o1/readgroup_fastq_se", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/bwa_o1/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o1/reference_sequence", | |
| "source": "#transform.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o1/readgroup_fastq_se", | |
| "source": "#transform.cwl/merge_o1_fastq_records/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o1/thread_count", | |
| "source": "#transform.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/bwa_o1/bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o1/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o2", | |
| "run": "#bwa_se.cwl", | |
| "scatter": "#transform.cwl/bwa_o2/readgroup_fastq_se", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/bwa_o2/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o2/reference_sequence", | |
| "source": "#transform.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o2/readgroup_fastq_se", | |
| "source": "#transform.cwl/merge_o2_fastq_records/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o2/thread_count", | |
| "source": "#transform.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/bwa_o2/bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/bwa_o2/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_pe", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_pe/source_sqlite", | |
| "source": "#transform.cwl/bwa_pe/sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_pe/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_pe/destination_sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_pe/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_se", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_se/source_sqlite", | |
| "source": "#transform.cwl/bwa_se/sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_se/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_se/destination_sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_sqlite_bwa_se/log" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_mergesamfiles", | |
| "run": "#picard_mergesamfiles_aoa.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/picard_mergesamfiles/INPUT", | |
| "source": [ | |
| "#transform.cwl/bwa_pe/bam", | |
| "#transform.cwl/bwa_se/bam", | |
| "#transform.cwl/bwa_o1/bam", | |
| "#transform.cwl/bwa_o2/bam" | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_mergesamfiles/OUTPUT", | |
| "source": "#transform.cwl/bam_name" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/picard_mergesamfiles/MERGED_OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/bam_reheader", | |
| "run": "#bam_reheader.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/bam_reheader/input", | |
| "source": "#transform.cwl/picard_mergesamfiles/MERGED_OUTPUT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/bam_reheader/output" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates", | |
| "run": "#conditional_markduplicates.cwl", | |
| "scatter": "#transform.cwl/conditional_markduplicates/run_markduplicates", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates/bam", | |
| "source": "#transform.cwl/bam_reheader/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates/run_markduplicates", | |
| "source": "#transform.cwl/run_markduplicates" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_markduplicates/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_index", | |
| "run": "#conditional_bamindex.cwl", | |
| "scatter": "#transform.cwl/conditional_index/run_bamindex", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/conditional_index/bam", | |
| "source": "#transform.cwl/bam_reheader/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_index/run_bamindex", | |
| "source": "#transform.cwl/run_bamindex" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_index/thread_count", | |
| "source": "#transform.cwl/thread_count" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/conditional_index/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/conditional_index/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index", | |
| "run": "#decider_conditional_bams.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/conditional_bam1", | |
| "source": "#transform.cwl/conditional_markduplicates/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/conditional_sqlite1", | |
| "source": "#transform.cwl/conditional_markduplicates/sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/conditional_bam2", | |
| "source": "#transform.cwl/conditional_index/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/conditional_sqlite2", | |
| "source": "#transform.cwl/conditional_index/sqlite" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/decide_markduplicates_index/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/gatk_baserecalibrator", | |
| "run": "#gatk4_baserecalibrator.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/gatk_baserecalibrator/input", | |
| "source": "#transform.cwl/decide_markduplicates_index/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/gatk_baserecalibrator/known-sites", | |
| "source": "#transform.cwl/known_snp" | |
| }, | |
| { | |
| "id": "#transform.cwl/gatk_baserecalibrator/reference", | |
| "source": "#transform.cwl/reference_sequence" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/gatk_baserecalibrator/output_grp" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/gatk_applybqsr", | |
| "run": "#gatk4_applybqsr.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/gatk_applybqsr/input", | |
| "source": "#transform.cwl/decide_markduplicates_index/output" | |
| }, | |
| { | |
| "id": "#transform.cwl/gatk_applybqsr/bqsr-recal-file", | |
| "source": "#transform.cwl/gatk_baserecalibrator/output_grp" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/gatk_applybqsr/output_bam" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr", | |
| "run": "#picard_validatesamfile.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr/INPUT", | |
| "source": "#transform.cwl/gatk_applybqsr/output_bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr/VALIDATION_STRINGENCY", | |
| "valueFrom": "STRICT" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr/OUTPUT" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite", | |
| "run": "#picard_validatesamfile_to_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/bam", | |
| "source": "#transform.cwl/gatk_applybqsr/output_bam", | |
| "valueFrom": "$(self.basename)" | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/input_state", | |
| "valueFrom": "gatk_applybqsr_readgroups" | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/metric_path", | |
| "source": "#transform.cwl/picard_validatesamfile_bqsr/OUTPUT" | |
| }, | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics", | |
| "run": "#metrics.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/metrics/bam", | |
| "source": "#transform.cwl/gatk_applybqsr/output_bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/amplicon_kit_set_file_list", | |
| "source": "#transform.cwl/amplicon_kit_set_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/capture_kit_set_file_list", | |
| "source": "#transform.cwl/capture_kit_set_file_list" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/common_biallelic_vcf", | |
| "source": "#transform.cwl/common_biallelic_vcf" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/fasta", | |
| "source": "#transform.cwl/reference_sequence" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/input_state", | |
| "valueFrom": "gatk_applybqsr_readgroups" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| }, | |
| { | |
| "id": "#transform.cwl/metrics/known_snp", | |
| "source": "#transform.cwl/known_snp" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/metrics/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/integrity", | |
| "run": "#integrity.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/integrity/bai", | |
| "source": "#transform.cwl/gatk_applybqsr/output_bam", | |
| "valueFrom": "$(self.secondaryFiles[0])" | |
| }, | |
| { | |
| "id": "#transform.cwl/integrity/bam", | |
| "source": "#transform.cwl/gatk_applybqsr/output_bam" | |
| }, | |
| { | |
| "id": "#transform.cwl/integrity/input_state", | |
| "valueFrom": "gatk_applybqsr_readgroups" | |
| }, | |
| { | |
| "id": "#transform.cwl/integrity/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/integrity/sqlite" | |
| } | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_all_sqlite", | |
| "run": "#merge_sqlite.cwl", | |
| "in": [ | |
| { | |
| "id": "#transform.cwl/merge_all_sqlite/source_sqlite", | |
| "source": [ | |
| "#transform.cwl/merge_sqlite_fastq_clean_pe/destination_sqlite", | |
| "#transform.cwl/merge_sqlite_fastq_clean_se/destination_sqlite", | |
| "#transform.cwl/merge_sqlite_bwa_pe/destination_sqlite", | |
| "#transform.cwl/merge_sqlite_bwa_se/destination_sqlite", | |
| "#transform.cwl/decide_markduplicates_index/sqlite", | |
| "#transform.cwl/picard_validatesamfile_bqsr_to_sqlite/sqlite", | |
| "#transform.cwl/metrics/sqlite", | |
| "#transform.cwl/integrity/sqlite" | |
| ] | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_all_sqlite/job_uuid", | |
| "source": "#transform.cwl/job_uuid" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#transform.cwl/merge_all_sqlite/destination_sqlite" | |
| }, | |
| { | |
| "id": "#transform.cwl/merge_all_sqlite/log" | |
| } | |
| ] | |
| } | |
| ], | |
| "id": "#transform.cwl" | |
| } | |
| ], | |
| "cwlVersion": "v1.0" | |
| } |
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