@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix EnvVarRequirement: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix InlineJavascriptRequirement: . @prefix sld: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix EnvironmentDef: . @prefix Dirent: . @prefix cwl: . @prefix ResourceRequirement: . @prefix CommandLineTool: . @prefix ExpressionTool: . cwl:default "QCFAIL,SECONDARY,SUPPLEMENTARY" ; cwl:inputBinding [ CommandLineBinding:prefix "exclude=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type . sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:long . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source , . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:long . cwl:in , ; cwl:out , ; cwl:run . sld:type xsd:string . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--tmp-dir" ] ; sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default "SILENT" . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 99 ] ; cwl:inputBinding [ CommandLineBinding:position 99 ] ; cwl:inputBinding [ CommandLineBinding:position 99 ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:default "fastq" ; cwl:inputBinding [ CommandLineBinding:prefix "--format" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--format" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--format" ] ; sld:type xsd:string . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . sld:type xsd:string . sld:type . cwl:inputBinding [ CommandLineBinding:prefix "-R" ] ; sld:type cwl:File . sld:type xsd:long . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_bam)" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:default "stats" ; cwl:inputBinding [ CommandLineBinding:prefix "--metric_name" ] ; sld:type xsd:string . sld:type xsd:long . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "null" , "ALL_READS" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl: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.fastq1.nameroot.split('_').slice(0,4).join('_') + \".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" ] ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax "$(inputs.thread_count)" ; ResourceRequirement:coresMin "$(inputs.thread_count)" ; ResourceRequirement:outdirMax "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil(2 * (inputs.fastq1.size + inputs.fastq2.size) / 1048576))" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bwa:{{ bwa }}" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "TARGET_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/fastqc" ) ; cwl:baseCommand ( "/usr/local/bin/fastqc" ) ; cwl:baseCommand ( "/usr/local/bin/fastqc" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax "$(inputs.threads)" ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 50 ; ResourceRequirement:tmpdirMin 50 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc:{{ fastqc }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc:{{ fastqc }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc:{{ fastqc }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax "$(inputs.threads)" ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 50 ; ResourceRequirement:tmpdirMin 50 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax "$(inputs.threads)" ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 50 ; ResourceRequirement:tmpdirMin 50 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:default "coordinate" ; cwl:inputBinding [ CommandLineBinding:prefix "SORT_ORDER=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:default "upload" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/biobambam/bin/bamtofastq" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil(0.9 * inputs.filename.size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil(0.9 * inputs.filename.size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil(0.9 * inputs.filename.size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil(0.9 * inputs.filename.size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/biobambam2:{{ biobambam }}" ] . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input.nameroot + \"_bqsr.grp\")" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--fastq" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--fastq" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self.capture_kit_target_uuid)" . cwl:source . cwl:default 200 ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "COVERAGE_CAP=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--reference" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*_2.fq.gz" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "NONE" ; cwl:inputBinding [ CommandLineBinding:prefix "INDEX_VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).db" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectWgsMetrics.log\")" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".idxstats\")" ] ; sld:type cwl:File . cwl:in ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "ValidateSamFile" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] . cwl:source ; cwl:valueFrom "$(self.capture_kit_target_file)" . cwl:valueFrom "lenient" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:long . cwl:source ; cwl:valueFrom "$(self.readgroup_meta_list)" . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type . cwl:source . cwl:source . sld:fields , ; sld:type sld:record . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out , ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . sld:type . cwl:source . cwl:default "_s.fq.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroupsuffixS=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "filename=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:long . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:valueFrom "markduplicates_readgroups" . cwl:source ; cwl:valueFrom "$(self.basename).hsmetrics" . cwl:source . cwl:source . sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--source_sqlite" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--variant" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:valueFrom "gdc_bam_o2" . sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "CONTEXTS=" ; CommandLineBinding:separate false ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:in , ; cwl:out , ; cwl:run . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . sld:type . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "BAIT_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_json" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--input_json" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; sld:type xsd:string . cwl:in , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . sld:type xsd:long . sld:type xsd:string . sld:fields , , , , , , , , , , , ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "output.log" ] ; sld:type cwl:File . sld:type xsd:long . cwl:source . sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source . sld:fields , ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:source . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "--threads" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--threads" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--threads" ] ; sld:type xsd:long . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--bqsr-recal-file" ] ; sld:type cwl:File . cwl:source . cwl:default "tempfq" ; cwl:inputBinding [ CommandLineBinding:prefix "T=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.OUTBAM)" ] ; sld:type cwl:File . cwl:source . cwl:default "_2.fq.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroupsuffixF2=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . cwl:source ; cwl:valueFrom "$(self.nameroot)" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:long . cwl:default 500000 ; cwl:inputBinding [ CommandLineBinding:prefix "--reads_in_memory" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--reads_in_memory" ] ; sld:type xsd:long . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_bam.basename.slice(0,-4) + '.bai')" ] ) ; cwl:baseCommand ( "samtools" "index" "-b" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function fastq_files_size(forward, reverse) {\n var divisor = 1048576;\n if (reverse == null) {\n return Math.ceil(forward.size / divisor)\n } else {\n return Math.ceil((forward.size + reverse.size) / divisor)\n }\n}\n" , "function file_size_multiplier(fobj, mult) {\n mult = typeof mult !== 'undefined' ? mult : 1;\n var divisor = 1048576;\n return Math.ceil(mult * fobj.size / divisor);\n}\n" , "function sum_file_array_size(farr) {\n var divisor = 1048576;\n var total = 0;\n for (var i = 0; i cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.OUTPUT)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.fastq_file_size)" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--output" ; CommandLineBinding:separate true ; cwl:valueFrom "$(inputs.bam_nameroot + \"_contamination.table\")" ] ) ; cwl:baseCommand ( "CalculateContamination" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/gatk:{{ gatk }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.basename + \".oxometrics\")" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename).pcrmetrics" . cwl:default "strict" ; cwl:inputBinding [ CommandLineBinding:prefix "--mode" ] ; sld:type xsd:string . sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] . sld:type xsd:string . cwl:default "idxstats" ; cwl:inputBinding [ CommandLineBinding:prefix "--metric_name" ] ; sld:type xsd:string . sld:type xsd:string . sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.nameroot + \".metrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard:{{ picard }}" ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename)" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "METRICS_FILE=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.OUTBAM + \".metrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "MarkDuplicates" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function fastq_files_size(forward, reverse) {\n var divisor = 1048576;\n if (reverse == null) {\n return Math.ceil(forward.size / divisor)\n } else {\n return Math.ceil((forward.size + reverse.size) / divisor)\n }\n}\n" , "function file_size_multiplier(fobj, mult) {\n mult = typeof mult !== 'undefined' ? mult : 1;\n var divisor = 1048576;\n return Math.ceil(mult * fobj.size / divisor);\n}\n" , "function sum_file_array_size(farr) {\n var divisor = 1048576;\n var total = 0;\n for (var i = 0; i sld:type xsd:long . cwl:source , , , , , , , . cwl:default "32G" ; cwl:inputBinding [ CommandLineBinding:position -10 ; CommandLineBinding:prefix "-Xmx" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "collate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools_metrics_sqlite:{{ samtools_metrics_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:stdout "$(inputs.job_uuid)_samtools_stats.log" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid +\".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid +\".log\")" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . cwl:valueFrom "did" . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\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" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam_path" ] ; sld:type cwl:File . cwl:source . sld:type xsd:long . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:long . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:valueFrom "gdc_bam_se" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.bam)" . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:long . cwl:in , , , ; cwl:out ; cwl:run . cwl:default "LIBRARY" , "READ_GROUP" , "SAMPLE" , "ALL_READS" ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ; CommandLineBinding:separate false ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type xsd:long . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".metrics\")" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . sld:type cwl:File . sld:type . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.bam_file_size)" . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_gatk_CalculateContamination.log\")" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "MergeSamFiles" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function fastq_files_size(forward, reverse) {\n var divisor = 1048576;\n if (reverse == null) {\n return Math.ceil(forward.size / divisor)\n } else {\n return Math.ceil((forward.size + reverse.size) / divisor)\n }\n}\n" , "function file_size_multiplier(fobj, mult) {\n mult = typeof mult !== 'undefined' ? mult : 1;\n var divisor = 1048576;\n return Math.ceil(mult * fobj.size / divisor);\n}\n" , "function sum_file_array_size(farr) {\n var divisor = 1048576;\n var total = 0;\n for (var i = 0; i cwl:source . cwl:source . cwl:default 5 ; cwl:inputBinding [ CommandLineBinding:prefix "level=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.reverse_fastq_file_size)" . cwl:outputSource ; sld:type cwl:File . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--dir" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--dir" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source . cwl:default "null" , "ALL_READS" . cwl:source . sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:default "false" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATE_INDEX=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.json" ; CommandOutputBinding:outputEval "${\n var output_array = [];\n for (var i = 0; i < self.length; i++) {\n var data = self[i].contents;\n output_array.push(data);\n }\n return output_array;\n}\n" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default "48G" ; cwl:inputBinding [ CommandLineBinding:position -10 ; CommandLineBinding:prefix "-Xmx" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.OUTBAM + \".metrics\")" ] ; sld:type cwl:File . sld:type xsd:long . sld:type xsd:boolean . sld:type . cwl:source ; cwl:valueFrom "$(self.readgroup_meta)" . cwl:source . sld:type xsd:long . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "--input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid)_samtools_flagstat.log" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:source . sld:type xsd:long . sld:type xsd:string . cwl:default "SILENT" . sld:type xsd:string . cwl:default "VERBOSE" ; cwl:inputBinding [ CommandLineBinding:prefix "MODE=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . sld:type xsd:string . sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "true" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(inputs.fasta_fai)" ; cwl:entryname "$(inputs.fasta_fai.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta)" ; cwl:entryname "$(inputs.fasta.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_pac)" ; cwl:entryname "$(inputs.fasta_pac.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_sa)" ; cwl:entryname "$(inputs.fasta_sa.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_bwt)" ; cwl:entryname "$(inputs.fasta_bwt.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_ann)" ; cwl:entryname "$(inputs.fasta_ann.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_amb)" ; cwl:entryname "$(inputs.fasta_amb.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.fasta_dict)" ; cwl:entryname "$(inputs.fasta_dict.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 500 ; ResourceRequirement:ramMin 500 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--output" ; cwl:valueFrom "$(inputs.input.basename)" ] ) ; cwl:baseCommand ( "ApplyBQSR" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/gatk:{{ gatk }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "JAVA_TOOL_OPTIONS" ; EnvironmentDef:envValue "-Dsamjdk.compression_level=7" ] ] . cwl:default 250 ; cwl:inputBinding [ CommandLineBinding:position 18 ; CommandLineBinding:prefix "NEAR_DISTANCE=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 16 ; CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type xsd:string . cwl:default "queryname" . cwl:source . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--tmp-dir" ] ; sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out , ; cwl:run . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.zip" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.zip" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.zip" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . cwl:source . cwl:in , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "--emit-original-quals" ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type xsd:long . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "outputdir=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . sld:type xsd:long . cwl:in , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.forward_fastq)" . sld:type . cwl:source ; cwl:valueFrom "$(self.bam_uuid)" . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--contaminants" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--contaminants" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--contaminants" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid)_samtools_stats.log" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var bams = [];\n for(var i = 0; i < inputs.bam.length; i++) {\n for(var j = 0; j < inputs.bam[i].length; j++) {\n if(inputs.bam[i][j].size > 0) {\n bams.push(inputs.bam[i][j])\n }\n }\n }\n\n if( inputs.run_markdups ) {\n return({\n 'do_markdup_workflow': [1],\n 'skip_markdup_workflow': [],\n 'out_bam': bams\n });\n } else {\n return({\n 'do_markdup_workflow': [],\n 'skip_markdup_workflow': [1],\n 'out_bam': bams\n });\n }\n }\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:valueFrom "gdc_bam_pe" . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type xsd:long . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".flagstat\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.OUTPUT)" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self)/$(inputs.input.nameroot).bai" . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 21 ; CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "output.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.log" ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self)/$(inputs.input.basename)" . sld:fields , , , ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).log" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:long . cwl:source ; cwl:valueFrom "$(self.fastq_uuid)" . cwl:source . cwl:inputBinding [ cwl:loadContents true ; cwl:valueFrom "$(null)" ] ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--quiet" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--quiet" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--quiet" ] ; sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*_upload.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_upload.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_upload.json" ] ; sld:type cwl:File . sld:type xsd:long . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*_o2.fq.gz" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.amplicon_kit_amplicon_file)" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "false" ; cwl:inputBinding [ CommandLineBinding:prefix "ASSUME_SORTED=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.amplicon_kit_target_file)" . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "CREATE_INDEX=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.forward_fastq)" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:valueFrom "did" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fastq1.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fastq1.basename)" ] ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--nogroup" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nogroup" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nogroup" ] ; sld:type xsd:boolean . sld:type xsd:long . cwl:default "2G" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.readgroup_meta_list)" . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/fastq_cleaner/fastq_cleaner" ) ; cwl:baseCommand ( "/fastq_cleaner/fastq_cleaner" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function fastq_files_size(forward, reverse) {\n var divisor = 1048576;\n if (reverse == null) {\n return Math.ceil(forward.size / divisor)\n } else {\n return Math.ceil((forward.size + reverse.size) / divisor)\n }\n}\n" , "function file_size_multiplier(fobj, mult) {\n mult = typeof mult !== 'undefined' ? mult : 1;\n var divisor = 1048576;\n return Math.ceil(mult * fobj.size / divisor);\n}\n" , "function sum_file_array_size(farr) {\n var divisor = 1048576;\n var total = 0;\n for (var i = 0; i cwl:source ; cwl:valueFrom "$(self.reverse_fastq)" . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.amplicon_kit_amplicon_uuid)" . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source , . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.forward_fastq)" . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "idxstats" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools:{{ samtools }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".idxstats\")" . sld:fields , , ; sld:type sld:record . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".db\")" ] ; sld:type cwl:File . sld:type cwl:File . cwl:default 250 ; cwl:inputBinding [ CommandLineBinding:position 18 ; CommandLineBinding:prefix "NEAR_DISTANCE=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . cwl:source , , , . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).db" ] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:outputSource ; sld:type . cwl:inputBinding [ CommandLineBinding:position 19 ; CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).db" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid).db" ] ; sld:type cwl:File . sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . sld:type xsd:long . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bam_readgroup_to_json:{{ bam_readgroup_to_json }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bam_readgroup_to_json:{{ bam_readgroup_to_json }}" ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools:{{ samtools }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".flagstat\")" . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . sld:type cwl:File . sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.reverse_fastq)" . cwl:in , ; cwl:out , ; cwl:run . cwl:in ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var output_value = JSON.parse(inputs.input.contents)[inputs.key];\n return {'output': output_value};\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:long . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.capture_kit_bait_uuid)" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.OUTPUT)" ] ; sld:type cwl:File . sld:type xsd:long . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "json_to_sqlite" ) ; cwl:baseCommand ( "json_to_sqlite" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/json-to-sqlite:{{ json_to_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/json-to-sqlite:{{ json_to_sqlite }}" ] . sld:type xsd:long . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--fastq2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--fastq2" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . sld:fields , , ; sld:type sld:record . cwl:outputSource ; sld:type . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--nano" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nano" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nano" ] ; sld:type xsd:boolean . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.basename + \".metrics\")" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , ; cwl:run . cwl:in , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 21 ; CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:default "SILENT" . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:source . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "USE_THREADING=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "CLIP_OVERLAPPING_READS=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:default "strict" ; cwl:inputBinding [ CommandLineBinding:prefix "--mode" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--mode" ] ; sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--outdir" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--outdir" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--outdir" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . sld:fields , ; sld:type sld:record . cwl:default "_o1.fq.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroupsuffixO=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--tmp-dir" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--upload_key" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--upload_key" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--upload_key" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source , , . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; sld:type cwl:File . sld:type xsd:string . cwl:default "false" ; cwl:inputBinding [ CommandLineBinding:prefix "MERGE_SEQUENCE_DICTIONARIES=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroup=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . sld:type xsd:long . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 20 ; CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.readgroup_meta)" . sld:type xsd:long . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "TARGET_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:source . sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:long . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:source . sld:type . cwl:outputSource ; sld:type . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--nofilter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nofilter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--nofilter" ] ; sld:type xsd:boolean . cwl:source . sld:type xsd:long . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:long . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:outputSource ; sld:type xsd:string . cwl:source . sld:type xsd:long . sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "ASSUME_SORT_ORDER=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:long . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:default 1 ; sld:type xsd:long . cwl:source . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n if( inputs.reverse_fastq ) {\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 }\n else {\n var output = { \"forward_fastq\": inputs.forward_fastq,\n \"readgroup_meta\": inputs.readgroup_meta\n };\n output.forward_fastq.format = \"edam:format_2182\";\n }\n return {'output': output}\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "gz=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -9 ; cwl:valueFrom "-jar" ] [ CommandLineBinding:position -8 ; cwl:valueFrom "/usr/local/bin/picard.jar" ] [ CommandLineBinding:position -7 ; cwl:valueFrom "CollectHsMetrics" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1000 ; ResourceRequirement:outdirMin 1000 ; ResourceRequirement:ramMax 49152 ; ResourceRequirement:ramMin 49152 ; ResourceRequirement:tmpdirMax 1000 ; ResourceRequirement:tmpdirMin 1000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard:{{ picard }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--input" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.forward_fastq)" . cwl:source ; cwl:valueFrom "$(self.readgroup_meta)" . cwl:default "LIBRARY" , "READ_GROUP" , "SAMPLE" , "ALL_READS" ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ; CommandLineBinding:separate false ] ; sld:items xsd:string ; sld:type sld:array ] . sld:type . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:default 3 ; sld:type xsd:long . cwl:source . cwl:source . cwl:source . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--upload-bucket" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--upload-bucket" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--upload-bucket" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "MarkDuplicates" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] . cwl:source . cwl:source . cwl:source . sld:type xsd:string . sld:type xsd:string . cwl:outputSource ; sld:type . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--output" ; CommandLineBinding:separate true ; cwl:valueFrom "$(inputs.input.nameroot + \"_bqsr.grp\")" ] ) ; cwl:baseCommand ( "BaseRecalibrator" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/gatk:{{ gatk }}" ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/readgroup_json_db:{{ readgroup_json_db }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/readgroup_json_db:{{ readgroup_json_db }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectHsMetrics.log\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:valueFrom "STRICT" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMin "${\nvar req_space = 0;\nfor (var i = 0; i < inputs.source_sqlite.length; i++) {\n req_space += inputs.source_sqlite[i].size;\n }\nreturn Math.ceil(req_space / 1048576);\n}\n" ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "${\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" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/merge-sqlite:{{ merge_sqlite }}" ] . cwl:source . cwl:source , . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type xsd:string . sld:type xsd:long . cwl:source . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--casava" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--casava" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--casava" ] ; sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "USE_OQ=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:default ; sld:type cwl:File . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "tryoq=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 20 ; CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , , , , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--sqlite_path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--sqlite_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type xsd:string . cwl:default "flagstat" ; cwl:inputBinding [ CommandLineBinding:prefix "--metric_name" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.INPUT.nameroot + \".stats\")" ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . sld:type . sld:type xsd:string . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:inputBinding [ CommandLineBinding:prefix "--limits" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--limits" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--limits" ] ; sld:type cwl:File , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "CollectHsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:type xsd:long . cwl:source . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type cwl:File . sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:source . sld:type xsd:boolean . cwl:source ; cwl:valueFrom "$(self.basename)" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; CommandLineTool:successCodes 3 , 2 , 0 ; cwl:arguments ( [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.basename + \".metrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "ValidateSamFile" "IS_BISULFITE_SEQUENCED=false" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard:{{ picard }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1000 ; ResourceRequirement:outdirMin 1000 ; ResourceRequirement:ramMax 5000 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMax 1000 ; ResourceRequirement:tmpdirMin 1000 ] . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.readgroup_meta_list)" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 22 ; CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . sld:type . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "--tmp-dir" ] ; sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . sld:type xsd:boolean . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fastq1.nameroot.split('_').slice(0,4).join('_') + \".bam\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_nameroot + \"_contamination.table\")" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 99 ] ; cwl:inputBinding [ CommandLineBinding:position 99 ] ; cwl:inputBinding [ CommandLineBinding:position 99 ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:source . sld:type . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . sld:type . cwl:outputBinding [ CommandOutputBinding:glob "*_1.fq.gz" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:long . cwl:default "SILENT" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_MarkDuplicates.log\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectTargetedPcrMetrics.log\")" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.capture_kit_bait_file)" . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.basename)" . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--extract" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--extract" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--extract" ] ; sld:type xsd:boolean . sld:type xsd:string . sld:type xsd:long . cwl:in , ; cwl:out , , ; cwl:run . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:valueFrom "gatk_applybqsr_readgroups" . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*.json" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.json" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out , , ; cwl:run . cwl:source . sld:type xsd:string . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:items xsd:long ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.readgroup_meta_list)" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_ValidateSamFile.log\")" ] ; sld:type cwl:File . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . sld:type [ sld:items ; sld:type sld:array ] . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--json_path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--json_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:position 25 ; CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ cwl:loadContents true ; cwl:valueFrom "$(null)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:valueFrom "gdc_bam_o1" . cwl:default 7 ; cwl:inputBinding [ CommandLineBinding:prefix "--kmers" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--kmers" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--kmers" ] ; sld:type xsd:long . cwl:source . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools:{{ samtools }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMin "$(Math.ceil((2 * inputs.input_bam.size) / 1048576))" ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMin "$(Math.ceil((2 * inputs.input_bam.size) / 1048576))" ] . cwl:source . sld:fields , , , , ; sld:type sld:record . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--output" ; CommandLineBinding:separate true ; cwl:valueFrom "$(inputs.input.nameroot + \"_pileupsummaries.table\")" ] [ CommandLineBinding:prefix "--intervals" ; cwl:valueFrom "$(inputs.variant)" ] ) ; cwl:baseCommand ( "GetPileupSummaries" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/gatk:{{ gatk }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--INPUT" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--INPUT" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--INPUT" ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.readgroup_meta)" . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:default "tmp_srt" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-T" ] ; sld:type xsd:string . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "stats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools:{{ samtools }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMin 5000 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:stdout "$(inputs.INPUT.nameroot + \".stats\")" . cwl:inputBinding [ CommandLineBinding:prefix "--input" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input.nameroot + \"_pileupsummaries.table\")" ] ; sld:type cwl:File . cwl:source . sld:type . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.INPUT.basename + \".oxometrics\")" ] ) ; cwl:baseCommand ( "java" "-jar" "/usr/local/bin/picard.jar" "CollectOxoGMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard:{{ picard }}" ] . cwl:default 100 ; cwl:inputBinding [ CommandLineBinding:prefix "MAX_OUTPUT=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "CLIP_OVERLAPPING_READS=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--table_name" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--table_name" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--adapters" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--adapters" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--adapters" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.reverse_fastq_uuid)" . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".log\")" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools_metrics_sqlite:{{ samtools_metrics_sqlite }}" ] ; cwl:stdout "$(inputs.job_uuid)_samtools_idxstats.log" . cwl:source . sld:fields , , , ; sld:type sld:record . cwl:source . cwl:default "CCG" . cwl:source . sld:type xsd:long . cwl:valueFrom "lenient" . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.reverse_fastq)" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "true" ) ; cwl:baseCommand ( "true" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(inputs.vcf_index)" ; cwl:entryname "$(inputs.vcf_index.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.vcf)" ; cwl:entryname "$(inputs.vcf.basename)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 500 ; ResourceRequirement:ramMin 500 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 500 ; ResourceRequirement:ramMin 500 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(inputs.vcf_index)" ; cwl:entryname "$(inputs.vcf_index.basename)" ] ; cwl:listing [ cwl:entry "$(inputs.vcf)" ; cwl:entryname "$(inputs.vcf.basename)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:in , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items xsd:long ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n var res = inputs.fastq2 === null ? null : inputs.fastq2.basename;\n return res;\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var res = inputs.fastq2 === null ? null : inputs.fastq2.basename;\n return res;\n }\n" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:default 10000 ; cwl:inputBinding [ CommandLineBinding:position 23 ; CommandLineBinding:prefix "SAMPLE_SIZE=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.readgroup_meta_list)" . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc_to_json:{{ fastqc_to_json }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc_to_json:{{ fastqc_to_json }}" ] . cwl:in ; cwl:out , , , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . sld:type xsd:string . a cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*_s.fq.gz" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid + \".db\")" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "gatk_CalculateContamination" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] . cwl:in , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid+\"_picard_CollectOxoGMetrics.log\")" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bam_readgroup_to_json:{{ bam_readgroup_to_json }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:type xsd:long . sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--known-sites" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var output = [];\n for (var i = 0; i < inputs.input.length; i++) {\n var readgroup_array = inputs.input[i];\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" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 22 ; CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl: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.fastq.nameroot.split('_').slice(0,4).join('_') + \".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" ] ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bwa:{{ bwa }}" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax "$(inputs.thread_count)" ; ResourceRequirement:coresMin "$(inputs.thread_count)" ; ResourceRequirement:outdirMax "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))" ; ResourceRequirement:ramMax 10000 ; ResourceRequirement:ramMin 10000 ; ResourceRequirement:tmpdirMax "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil(2 * (inputs.fastq.size) / 1048576))" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "BAIT_SET_NAME=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -9 ; cwl:valueFrom "-jar" ] [ CommandLineBinding:position -8 ; cwl:valueFrom "/usr/local/bin/picard.jar" ] [ CommandLineBinding:position -7 ; cwl:valueFrom "CollectTargetedPcrMetrics" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard:{{ picard }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1000 ; ResourceRequirement:outdirMin 1000 ; ResourceRequirement:ramMax 32768 ; ResourceRequirement:ramMin 32768 ; ResourceRequirement:tmpdirMax 1000 ; ResourceRequirement:tmpdirMin 1000 ] . cwl:source . cwl:default "true" ; cwl:inputBinding [ CommandLineBinding:prefix "IGNORE_WARNINGS=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type . cwl:source ; cwl:valueFrom "$(self.amplicon_kit_target_uuid)" . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--job_uuid" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self)/$(inputs.input.basename)" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "AMPLICON_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--config-file" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--config-file" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--config-file" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "result.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "result.json" ] ; sld:type cwl:File . cwl:source . cwl:default "download" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "CollectTargetedPcrMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 10 ; ResourceRequirement:tmpdirMin 10 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 19 ; CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool: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" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] . cwl:source . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:position 25 ; CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.basename)" . sld:type xsd:long , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.job_uuid)_samtools_idxstats.log" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . sld:type [ sld:items [ sld:items ; sld:type sld:array ] ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:long . cwl:source . sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.basename)" . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:long . sld:type xsd:long . sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--input" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "_o2.fq.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroupsuffixO2=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:valueFrom "lenient" . cwl:source . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n // /begin chakrit / CC-BY-SA-4.0\n // https://stackoverflow.com/a/2548133/810957\n function endsWith(str, suffix) {\n return str.indexOf(suffix, str.length - suffix.length) !== -1;\n }\n // /end chakrit / CC-BY-SA-4.0\n\n // /begin 3DFace / CC-BY-SA-4.0\n // https://stackoverflow.com/questions/3820381/need-a-basename-function-in-javascript#comment29942319_15270931\n function local_basename(path) {\n var basename = decodeURIComponent(path.split(/[\\\\/]/).pop());\n return basename\n }\n // /end 3DFace / CC-BY-SA-4.0\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 readgroup name from fastq\n function fastq_to_rg_id(fq_file_object) {\n var fastq_name = local_basename(fq_file_object.location);\n var slice_number = get_slice_number(fastq_name);\n var readgroup_name = fastq_name.slice(0,slice_number);\n return readgroup_name;\n }\n\n function load_bamrgs() {\n var res = [];\n for (var i = 0; i < inputs.bam_readgroup_contents.length; i++) {\n var curr = JSON.parse(inputs.bam_readgroup_contents[i]);\n res.push(curr);\n }\n return(res);\n }\n\n function find_graph_rg(bam_rgid) {\n for (var i = 0; i < inputs.readgroup_meta_list.length; i++) {\n var record = inputs.readgroup_meta_list[i];\n if (record[\"ID\"] === bam_rgid) {\n return(record);\n }\n }\n return(null);\n }\n\n function find_bam_rg(bam_meta, rgid) {\n for (var i = 0; i < bam_meta.length; i++) {\n var record = bam_meta[i];\n if (record[\"ID\"] === rgid) {\n return(record);\n }\n }\n return(null);\n }\n\n function make_record(readgroup_meta, forward_fastq, reverse_fastq) {\n var output = {\"forward_fastq\": forward_fastq,\n \"reverse_fastq\": reverse_fastq,\n \"readgroup_meta\": readgroup_meta};\n output.forward_fastq.format = \"edam:format_2182\";\n if(reverse_fastq !== null) {\n output.reverse_fastq.format = \"edam:format_2182\";\n }\n return(output);\n }\n\n function normalize_record(record) {\n // first meta_rg has right sample\n var first_rg = inputs.readgroup_meta_list[0];\n var first_sm = first_rg['SM'];\n var first_pl = first_rg['PL'].toUpperCase();\n\n if(!record.readgroup_meta.hasOwnProperty('SM') || record.readgroup_meta['SM'] !== first_sm) {\n record.readgroup_meta['SM'] = first_sm;\n }\n\n if(!record.readgroup_meta.hasOwnProperty('LB') || record.readgroup_meta['LB'] === null) {\n record.readgroup_meta['LB'] = first_sm;\n }\n\n if(!record.readgroup_meta.hasOwnProperty('PL') || record.readgroup_meta['PL'] === null) {\n record.readgroup_meta['PL'] = first_pl;\n } else {\n record.readgroup_meta['PL'] = record.readgroup_meta['PL'].toUpperCase();\n }\n }\n\n // output\n var output_array = [];\n\n // bam rgs\n var bam_meta = load_bamrgs();\n\n // get readgroup names from fastq, lookup in graph, lookup in bam meta\n // if needed.\n for (var i = 0; i < inputs.forward_fastq_list.length; i++) {\n var fq = inputs.forward_fastq_list[i];\n var rev_fq = inputs.reverse_fastq_list.length > 0 ? inputs.reverse_fastq_list[i] : null;\n var readgroup_name = fastq_to_rg_id(fq);\n\n // try to look up in the graph metadata using rgname as both rgid and rgpu\n var graph_rg = find_graph_rg(readgroup_name);\n if (graph_rg !== null) {\n var rec = make_record(graph_rg, fq, rev_fq);\n normalize_record(rec);\n output_array.push(rec);\n }\n else {\n // Match with bam meta, try to lookup from PU if possible\n var bam_rg = find_bam_rg(bam_meta, readgroup_name);\n if(bam_rg === null) {\n throw \"Unable to find the matching bam RG record\";\n }\n var rec = make_record(bam_rg, fq, rev_fq);\n normalize_record(rec);\n output_array.push(rec);\n }\n }\n return {'output': output_array};\n }\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "--metric_name" "CollectOxoGMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/picard_metrics_sqlite:{{ picard_metrics_sqlite }}" ] . cwl:in ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n if(inputs.markdup_bam.length == 1) {\n return({'bam': inputs.markdup_bam[0],\n 'sqlite': inputs.markdup_sqlite[0]});\n } else if(inputs.skip_markdup_bam.length == 1) {\n return({'bam': inputs.skip_markdup_bam[0],\n 'sqlite': null})\n } else {\n throw \"Either markdup bam or skip markdup bam arrays have to be length 1\"\n }\n }\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:default "bam" ; cwl:inputBinding [ CommandLineBinding:prefix "inputformat=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:source ; cwl:valueFrom "${\n if (self) {\n return([1]);\n } else {\n return([]);\n }\n }\n" . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:valueFrom "did" . cwl:source ; cwl:valueFrom "$(self.forward_fastq_uuid)" . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] . sld:type xsd:long . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "CUSTOM_AMPLICON_SET_NAME=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , , , , , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , , , , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 5 ; ResourceRequirement:outdirMin 5 ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax 5 ; ResourceRequirement:tmpdirMin 5 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/samtools_metrics_sqlite:{{ samtools_metrics_sqlite }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.job_uuid)_samtools_flagstat.log" . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--input_state" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n function rename(root, index, suffix) {\n var n = root.toString() + \"_\" + index.toString() + suffix\n return n\n }\n var i = inputs.tag\n var output = [];\n var suffixes = [\n \"_1.fq.gz\",\n \"_2.fq.gz\",\n \"_o1.fq.gz\",\n \"_o2.fq.gz\",\n \"_s.fq.gz\"\n ]\n for (var j = 0; j < inputs.input.length; j++) {\n var readgroup = inputs.input[j];\n var foward_fq = readgroup[\"forward_fastq\"][\"basename\"]\n for (var k = 0; k < suffixes.length; k++) {\n if (foward_fq.endsWith(suffixes[k])) {\n readgroup[\"forward_fastq\"][\"basename\"] = rename(i, j, suffixes[k]);\n }\n }\n if (readgroup[\"reverse_fastq\"]){\n var reverse_fq = readgroup[\"reverse_fastq\"][\"basename\"]\n for (var k = 0; k < suffixes.length; k++) {\n if (reverse_fq.endsWith(suffixes[k])) {\n readgroup[\"reverse_fastq\"][\"basename\"] = rename(i, j, suffixes[k]);\n }\n }\n }\n output.push(readgroup);\n }\n return {'output': output}\n }\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.secondaryFiles[0])" . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type . cwl:outputSource ; sld:type cwl:File . cwl:default "STRICT" ; cwl:inputBinding [ CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc_db:{{ fastqc_db }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 100 ; ResourceRequirement:tmpdirMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 100 ; ResourceRequirement:tmpdirMin 100 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc_db:{{ fastqc_db }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/fastqc_db:{{ fastqc_db }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 10 ; ResourceRequirement:outdirMin 10 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 100 ; ResourceRequirement:tmpdirMin 100 ] . cwl:source . cwl:source . sld:type xsd:long . cwl:source ; cwl:valueFrom "$(self.bam)" . cwl:source ; cwl:valueFrom "$(self.readgroup_meta)" . sld:type cwl:File . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "TMP_DIR=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 16 ; CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "--metric_path" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "fastqc.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "fastqc.json" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:default "_1.fq.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "outputperreadgroupsuffixF=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:long . sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:default ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fastq.nameroot.split('_').slice(0,4).join('_') + \".bam\")" ] ; sld:type cwl:File . cwl:source , , , , , , ; cwl:valueFrom "${\n var res = [];\n for (var i = 0; i sld:type xsd:boolean . cwl:source . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:valueFrom "gatk_applybqsr_readgroups" . cwl:default 10000 ; cwl:inputBinding [ CommandLineBinding:position 23 ; CommandLineBinding:prefix "SAMPLE_SIZE=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "DB_SNP=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var output = { \"bam\": inputs.bam,\n \"readgroup_meta_list\": inputs.readgroup_meta_list};\n output.bam.format = \"edam:format_2572\";\n return {'output': output}\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , , ] . cwl:source . sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string . sld:type xsd:string . sld:type . cwl:source . cwl:source ; cwl:valueFrom "$(self.forward_fastq_file_size)" . cwl:inputBinding [ CommandLineBinding:prefix "--bam_path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--bam_path" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*_o1.fq.gz" ; CommandOutputBinding:outputEval "${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }) }\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type xsd:string . sld:type xsd:string . sld:type [ sld:items xsd:long ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "--noextract" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--noextract" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--noextract" ] ; sld:type xsd:boolean . cwl:source . sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . cwl:source ; cwl:valueFrom "${\n var res = self.reverse_fastq === null ? \"fastq_cleaner_se\" : \"fastq_cleaner_pe\";\n return(res);\n }\n" . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type . cwl:default 200 ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "COVERAGE_CAP=" ; CommandLineBinding:separate false ] ; sld:type xsd:long . cwl:source . cwl:source ; cwl:valueFrom "$(self.forward_fastq)" .