@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix ResourceRequirement: . @prefix ExpressionTool: . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "read1.fastq" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source , . sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "all_SI" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "File to be HLA-typed" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type cwl:Directory , xsd:string . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . rdfs:comment "a vcf file of known polymorphic sites for somalier to compare normal and tumor samples for identity; sites files can be found at: https://github.com/brentp/somalier/releases" ; sld:type cwl:File . cwl:valueFrom "annotated_filtered.vcf" . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default false ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "--normal-cov" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , , , ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--llr-threshold" ] ; sld:type xsd:float . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "per_chromosome_pindel.out" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "intervals_to_bed.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use feature qw(say);\n\nfor my $line (<>) {\n chomp $line;\n\n next if substr($line,0,1) eq '@'; #skip header lines\n\n my ($chrom, $start, $stop) = split(/\\t/, $line);\n say(join(\"\\t\", $chrom, $start-1, $stop));\n}\n" ; cwl:entryname "intervals_to_bed.pl" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:stdout "interval_list.bed" . cwl:source . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:source . sld:type xsd:float . cwl:source . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "add expression info to vcf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.expression.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.expression.vcf.gz" ] ) ; cwl:baseCommand ( "vcf-expression-annotator" ) ; cwl:baseCommand ( "vcf-expression-annotator" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".antitargetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string . rdfs:comment "Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)" ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--callRegions" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:source . cwl:outputSource ; 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:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions" ] ; sld:type cwl:Directory . cwl:source . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "bam_readcount 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 ] . rdfs:comment "Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample\n" ; rdfs:label "Sequencing per-target coverage summary of target intervals from tumor DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:int , sld:null . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--known-sites" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--known-sites" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--known-sites" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "bwa-indexed reference file" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "SelectVariants" ) ; 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 ; 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: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 ; 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:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:default "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . rdfs:comment "path to the vep cache directory, available at: https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre" ; sld:type cwl:Directory , xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source , ; cwl:valueFrom "${\n var normal = self[0];\n var fasta = self[1];\n return {'normal_bam': normal, 'fasta_file': fasta};\n}\n" . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$((inputs.reference.hasOwnProperty('cnn_file'))? null : '--normal')" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "batch" ) ; 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 "etal/cnvkit:0.9.5" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position -1 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1" ; cwl:default 0 ; sld:type xsd:float . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . rdfs:comment "Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample\n" ; rdfs:label "Sequencing coverage summary at target sites from tumor DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out , , ; cwl:run . cwl:source . cwl:default "indel" . cwl:source . 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 cwl:File . rdfs:comment "tumor_name provides a string for what the MT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n" ; rdfs:label "tumor_name: String specifying the name of the MT sample" ; cwl:default "tumor" ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:default 1.5e-01 ; sld:type xsd:float . cwl:in ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "used to provide clinical HLA typing results in the format HLA-X*01:02[/HLA-X...] when available." ; rdfs:label "Clinical HLA typing results, limited to MHC Class I alleles; element format: HLA-X*01:02[/HLA-X...]" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int . sld:type xsd:float , sld:null . cwl:source . sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Tab-delimited file containing transcript-level abundance estimates in TPM, created by kallisto\n" ; rdfs:label "Transcript-level abundance table by kallisto" ; cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . rdfs:comment "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1" ; cwl:default 1 ; sld:type xsd:float . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "all_LI" ] ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:string . cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "if true, outputs assembled contig sequences in final VCF files, in the INFO field CONTIG" ; cwl:inputBinding [ CommandLineBinding:position -7 ; CommandLineBinding:prefix "--outputContig" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Filter variants from the DoCM detector" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.outdir)/docm_filtered_variants.vcf" ) ; cwl:baseCommand ( "/usr/bin/perl" "docm_filter.pl" ) ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse feature qw(say);\n\ndie(\"Wrong number of arguments. Provide docm_vcf, normal_cram, tumor_cram, output_vcf_file, set_filter_flag\") unless scalar(@ARGV) == 5;\nmy ($docm_vcf, $normal_cram, $tumor_cram, $output_vcf_file, $set_filter_flag) = @ARGV;\n\nmy $samtools = '/opt/samtools/bin/samtools';\nmy $normal_header_str = `$samtools view -H $normal_cram`;\nmy $tumor_header_str = `$samtools view -H $tumor_cram`;\n\nmy ($normal_name) = $normal_header_str =~ /SM:([ -~]+)/;\nmy ($tumor_name) = $tumor_header_str =~ /SM:([ -~]+)/;\n\nunless ($normal_name and $tumor_name) {\n die \"Failed to get normal_name: $normal_name from $normal_cram AND tumor_name: $tumor_name from $tumor_cram\";\n}\n\nmy $docm_vcf_fh;\nif($docm_vcf =~ /.gz$/){\n open($docm_vcf_fh, \"gunzip -c $docm_vcf |\") or die(\"couldn't open $docm_vcf to read\");\n} else {\n open($docm_vcf_fh, $docm_vcf) or die(\"couldn't open $docm_vcf to read\");\n}\nopen(my $docm_out_fh, \">\", \"$output_vcf_file\") or die(\"couldn't open $output_vcf_file for write\");\n\nmy ($normal_index, $tumor_index);\n\nwhile (<$docm_vcf_fh>) {\n chomp;\n if (/^##/) {\n say $docm_out_fh $_;\n }\n elsif (/^#CHROM/) {\n if ($set_filter_flag) {\n say $docm_out_fh '##FILTER=';\n }\n my @columns = split /\\t/, $_;\n my %index = (\n $columns[9] => 9,\n $columns[10] => 10,\n );\n ($normal_index, $tumor_index) = map{$index{$_}}($normal_name, $tumor_name);\n unless ($normal_index and $tumor_index) {\n die \"Failed to get normal_index: $normal_index for $normal_name AND tumor_index: $tumor_index for $tumor_name\";\n }\n $columns[9] = $normal_name;\n $columns[10] = $tumor_name;\n my $header = join \"\\t\", @columns;\n say $docm_out_fh $header;\n }\n else {\n my @columns = split /\\t/, $_;\n my @tumor_info = split /:/, $columns[$tumor_index];\n my ($AD, $DP) = ($tumor_info[1], $tumor_info[2]);\n next unless $AD;\n my @AD = split /,/, $AD;\n shift @AD; #the first one is ref count\n \n for my $ad (@AD) {\n if ($ad > 5 and $ad/$DP > 0.01) {\n my ($normal_col, $tumor_col) = map{$columns[$_]}($normal_index, $tumor_index);\n $columns[9] = $normal_col;\n $columns[10] = $tumor_col;\n if ($set_filter_flag) {\n $columns[6] = 'DOCM_ONLY';\n }\n else {\n $columns[6] = '.';\n }\n my $new_line = join \"\\t\", @columns;\n say $docm_out_fh $new_line;\n last;\n }\n }\n }\n}\n\nclose($docm_vcf_fh);\nclose($docm_out_fh);\n" ; cwl:entryname "docm_filter.pl" ] ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . rdfs:comment "array of plugins to use when running vep" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Combine germline and somatic vcf for pVACseq phasing" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--assumeIdenticalSamples" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined_somatic_plus_germline.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; 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 "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:float , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude-filtered" ] ; sld:type sld:null , xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rf-stranded'];\n } else if (inputs.strand == 'second') {\n return ['--fr-stranded'];\n } else {\n return [];\n }\n } else {\n return [];\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; 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 ; 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:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-d" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pindel.noend.vcf.gz" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "mutect.filtered.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ; rdfs:label "Staged Renamer" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] . sld:fields , ; sld:type sld:record . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "TUMOR" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:default "final" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:in , , , , , , , , , , ; cwl:out , , , , , , , , , , , ; cwl:run . sld:type xsd:int . cwl:source . rdfs:label "custom annotation file to be used by vep" ; sld:fields , , ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . rdfs:label "Identify known variants colocated with input variant" ; sld:type xsd:boolean . sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/combined/$(inputs.sample_name).filtered.tsv" ] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "mutect parallel workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self).bam" . cwl:source . rdfs:comment "synonyms_file allows the use of different chromosome identifiers in vep inputs or annotation files (cache, database, GFF, custom file, fasta). File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2." ; sld:type cwl:File , sld:null . rdfs:comment "Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a normal DNA sample, for example to assess target coverage\n" ; rdfs:label "Sequencing coverage summary of target intervals from normal DNA" ; cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . rdfs:label "Force report the overlapping coordinates of custom feature instead of based on the exact coordinates" ; sld:type xsd:boolean . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:cwlVersion ; 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 ; 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 ; 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 ; 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 ; 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 ; 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 ; 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 ; 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 ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . rdfs:comment "Create a whole-genome copy ratio profile as a PDF scatter plot" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--scatter" ] ; sld:type xsd:boolean , sld:null . cwl:default "NORMAL" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.optitype_name)_coverage_plot.pdf" ] ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . cwl:in , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext === \".gz\"){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "annotated.coding_variant_filtered.vcf" ] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:callers" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . rdfs:comment "bqsr_intervals provides an array of genomic intervals for which to apply\nGATK base quality score recalibrations. Typically intervals are given\nfor the entire chromosome (i.e. chr1, chr2, etc.), these names should match\nthe format in the reference file.\n" ; rdfs:label "bqsr_intervals: Array of strings specifying regions for base quality score recalibration" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "merged.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; 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:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.txt" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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 ] . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "varscan somatic 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 , , , , , , , , , , , , , . a cwl:Workflow ; rdfs:label "exome alignment and germline variant detection, with optitype for HLA typing" ; 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:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . sld:type . cwl:valueFrom "annotated.filtered.final.tsv" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Run optitype on dna samples" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(runtime.tmpdir)" ] [ cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/bin/bash" "/usr/bin/optitype_script.sh" ) ; 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:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 20000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/immuno_tools-cwl:1.0.1" ] . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . a cwl:ExpressionTool ; ExpressionTool:expression "${\n var metrics = inputs.verify_bam_id_metrics.contents.split(\"\\n\");\n if ( metrics[0].split(\"\\t\")[6] == 'FREEMIX' ) {\n return {'freemix_score': metrics[1].split(\"\\t\")[6]};\n } else {\n return {'freemix_score:': null };\n }\n}\n" ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:valueFrom "somatic_indels" . cwl:in , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "Diagnosis/quality metrics specific for sequencing data generated through hybrid-selection (e.g. whole exome) from a tumor DNA sample, for example to assess target coverage of WES\n" ; rdfs:label "Sequencing coverage summary of target intervals from tumor DNA" ; cwl:outputSource ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "AD" , "GT" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "all_TD" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . cwl:valueFrom "ALL_READS" . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; 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:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] . cwl:source . cwl:source . sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "RIBOSOMAL_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "-1" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$( (self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/split_interval_list_to_bed_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] . a cwl:CommandLineTool ; rdfs:label "strelka 2.9.9" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "$(inputs.cpu_reserved)" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docker_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/strelka-cwl:2.9.9" ] . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:int , sld:null . cwl:default "NORMAL" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "exome alignment and germline variant detection" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . sld:type xsd:float , sld:null . sld:type cwl:File , sld:null . sld:type cwl:File . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Sambamba: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.cores)" "$(runtime.outdir)/merged.bam" ) ; cwl:baseCommand ( "/usr/bin/sambamba_merge" ) ; 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 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/biscuit:0.3.8.2" ] . cwl:source . a cwl:Workflow ; rdfs:label "HS Metrics workflow" ; ns1:original_cwlVersion "v1.2" ; 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: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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-G" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type cwl:File . cwl:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:type , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type sld:null , xsd:int . cwl:source . sld:type cwl:Directory , xsd:string . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . rdfs:comment "target_intervals is an interval_list corresponding to the targets for the capture reagent.\nBED files with this information can be converted to interval_lists with Picard BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n" ; rdfs:label "target_intervals: interval_list file of targets used in the sequencing experiment" ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_I/$(inputs.sample_name).filtered.tsv" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "used to provide clinical HLA typing results; separated from class I due to nomenclature inconsistencies" ; rdfs:label "Clinical HLA typing results, limited to MHC Class II alleles" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.interval_list.nameroot).expanded.interval_list" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:default 5e-02 ; sld:type xsd:float . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf_summary.html" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REF_FLAT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; sld:type cwl:File . cwl:default "snv" . cwl:outputSource ; 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 ] . rdfs:comment "Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a normal DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool\n" ; rdfs:label "Sequencign alignment summary from normal DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Previously discovered variants to be flagged in this pipelines's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . sld:type xsd:float , sld:null . cwl:source . sld:type xsd:float . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "read2.fastq" ] ; sld:type cwl:File . cwl:default "gene" . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Sequencing protocol used for input data" ; cwl:default "hybrid" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--method" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:comment "Summary with the count numbers of alignments for each FLAG type from a tumor DNA sample, including 13 categories based on the bit flags in the FLAG field\n" ; rdfs:label "Sequencing count metrics based on SAM FLAG field from tumor sample" ; cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_I/$(inputs.sample_name).all_epitopes.tsv" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Sample name to be replaced" ; 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 . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:default "NOPREFIX" ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:default 0 ; sld:type xsd:int , sld:null . sld:type xsd:boolean , sld:null . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "AF" , "TX" , "GX" , "RDP" , "RAF" , "AD" , "RAD" , "DP" , "GT" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Kallisto: TranscriptToGene" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/src/transcript_to_gene.R" ) ; cwl:baseCommand ( "/usr/local/bin/Rscript" ) ; 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 "mgibio/rnaseq:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 2000 ] . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "The names of one or more standard VCF fields or INFO fields to include in the output table" ; cwl:default "POS" , "ALT" , "ID" , "AF" , "AC" , "set" , "REF" , "CHROM" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:float . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 3 ; CommandLineBinding:prefix "" ; CommandLineBinding:separate false ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out , , , , , , , , , , ; cwl:run . cwl:in ; cwl:out ; cwl:run . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; 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 ; 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 ; 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 ; 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: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:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.file.basename).gz" . sld:type cwl:File . cwl:source . cwl:default "somatic_tumor_only" . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-I" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default 50 ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . rdfs:comment "Known polymorphic indels recommended by GATK for a variety of\ntools including the BaseRecalibrator. This is part of the GATK resource\nbundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213\nFile should be in vcf format, and tabix indexed.\n" ; rdfs:label "bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . rdfs:comment "Average size of split target bins (results are approximate)" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--target-avg-size" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default "REF" , "ALT" , "CHROM" , "ID" , "POS" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "HISAT2: align" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-p" "$(runtime.cores)" "--dta" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/usr/bin/sambamba" "view" "-S" "-f" "bam" "-l" "0" "/dev/stdin" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/usr/bin/sambamba" "sort" "-t" "$(runtime.cores)" "-m" "8G" "-o" "$(runtime.outdir)/aligned.bam" "/dev/stdin" ) ; cwl:baseCommand ( "/usr/bin/hisat2" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 16 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type , sld:null . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "create filtered VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; 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 "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . a cwl:CommandLineTool ; rdfs:label "StringTie" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" "$(runtime.outdir)/stringtie_transcripts.gtf" "-A" "$(runtime.outdir)/stringtie_gene_expression.tsv" "-p" "$(runtime.cores)" "-e" ) ; cwl:baseCommand ( "/usr/bin/stringtie" ) ; 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:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/fusion.txt" ] ; sld:type cwl:File . cwl:valueFrom "pindel" . cwl:source . cwl:default "AD" , "GT" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; 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 ] . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; 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:in , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "bam to trimmed fastqs and HISAT alignments" ; 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; 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:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:default true . cwl:source . a cwl:Workflow ; rdfs:label "exome alignment with qc" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; 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:SubworkflowFeatureRequirement ] . cwl:source . sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "tumor_sequence is a data structure described in sequence_data.yml used to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n" ; rdfs:label "tumor_sequence: file specifying the location of MT sequencing data" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--fasta" ] ; sld:type cwl:File , xsd:string . rdfs:comment "Sorted CRAM file of sequencing read alignments by bwa-mem from a tumor DNA sample with duplicate reads tagged\n" ; rdfs:label "Sorted CRAM from tumor DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type sld:null , xsd:boolean . rdfs:comment "roi_intervals is a list of regions (in interval_list format) within which to call somatic variants" ; rdfs:label "roi_intervals: regions of interest in which variants will be called" ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "filter variants at sites below a given sequence depth in each sample" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(runtime.outdir)/depth_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/depth_filter.py" ) ; 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:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/depth-filter:0.1.2" ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:fields ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:fields , ; sld:type sld:record . a cwl:Workflow ; rdfs:label "process VCF 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:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Picard: RNA Seq Metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "O=$(runtime.outdir)/rna_metrics.txt" ] [ cwl:valueFrom "CHART=$(runtime.outdir)/rna_metrics.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "CollectRnaSeqMetrics" ) ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 18000 ] . cwl:default 1e-03 ; sld:type xsd:float . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:default 5e-02 ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . sld:type , . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; 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 ; NetworkAccess:networkAccess true ] ; 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 "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:label "Annotation file type" ; sld:symbols , , , , ; sld:type sld:enum . cwl:default false . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:default 400 ; sld:type xsd:int . cwl:in , , , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_II/$(inputs.sample_name).all_epitopes.tsv" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:float . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "gene_abundance.tsv" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--adapter-trim-end" ] ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:comment "HDF5 binary file containing transcript-level abundance esimates, bootstrap estimate, and so on, created by kallisto\n" ; rdfs:label "Transcript-level abundance table in HDF5 format by kallisto" ; cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--net-chop-method" ] ; sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type cwl:File . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "pindel somatic filter v1" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/write_pindel_filter_config.pl" "$(inputs.pindel_output_summary.path)" "$(inputs.reference)" "$(runtime.outdir)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/perl" "/usr/bin/somatic_indelfilter.pl" "filter.config" ) ; 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 "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] . rdfs:comment "bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.\nThese are essentially coordinates for regions you were able to design probes for in the reagent.\nTypically the reagent provider has this information available in bed format and it can be\nconverted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo\nof baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data\n" ; rdfs:label "bait_intervals: interval_list file of baits used in the sequencing experiment" ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . a cwl:Workflow ; rdfs:comment "Some workflow engines won't stage files in our nested structure, so parse it out here" ; rdfs:label "adapter for sequence_align_and_tag" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps ; 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:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . a cwl:CommandLineTool ; rdfs:label "run bam-readcount" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:cwlVersion ; 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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:stdout "$(inputs.sample)_bam_readcount.tsv" . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "hla_calls" ] ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_1.fastq" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Summary with the count numbers of alignments for each FLAG type from a normal DNA sample, including 13 categories based on the bit flags in the FLAG field\n" ; rdfs:label "Sequencing count metrics based on SAM FLAG field from normal sample" ; cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "aligned.bam" ] ; sld:type cwl:File . cwl:default false ; sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . sld:type xsd:int . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:default "HGVSp" , "HGVSc" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . rdfs:comment "bgzip-compressed, tabix-indexed BED file specifiying regions to which manta structural variant analysis is limited" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "output.snp.vcf" ] ; sld:type cwl:File . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; 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:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Previously discovered variants to be flagged in this pipelines's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:valueFrom "somatic_hc_snvs" . cwl:source . rdfs:comment "VEP fields in final output" ; cwl:default "HGVSp" , "HGVSc" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; 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 ] . rdfs:comment "RNA-seq Diagnosis/quality metrics showing the distribution of the bases within the transcripts, created by picard CollectRnaSeqMetrics tool\n" ; rdfs:label "RNA-seq Diagnosis/quality metrics from tumor RNA" ; cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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 ] . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--trna-vaf" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".targetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "PDF file for the plot of RNA sequencing coverage at the normalized position across transcript as RNA-seq diagnosis/quality metrics, created by picard CollectRnaSeqMetrics tool\n" ; rdfs:label "Plot for RNA-seq diagnosis/quality metrics" ; cwl:outputSource ; sld:type cwl:File , sld:null . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "pindel parallel 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_gene_expression.tsv" ] ; sld:type cwl:File . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; 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:inputBinding [ CommandLineBinding:prefix "--allele-specific-binding-thresholds" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , ; cwl:run . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Sample name to replace the other" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-V" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; sld:type cwl:File . cwl:valueFrom "ALL_READS" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumorBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "chr20" , "chr5" , "chr19" , "chr21" , "chr11" , "chr7" , "chr12" , "chr1" , "chr15" , "chr22" , "chr8" , "chr13" , "chr16" , "chr9" , "chr14" , "chr17" , "chr10" , "chr18" , "chr2" , "chr3" , "chr6" , "chr4" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Sorted CRAM file of sequencing read alignments by bwa-mem from a normal DNA sample with duplicate reads tagged\n" ; rdfs:label "Sorted CRAM from normal DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/combined/$(inputs.sample_name).all_epitopes.tsv" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "verifyBamID output files containing the contamination estimate in a tumor DNA sample, across all readGroups and per readGroup separately\n" ; rdfs:label "Sequencing quality assessment metric for tumor sample contamination" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "${ var prefix = self !== null ? self : \"\"; if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return prefix + inputs.intervals[0] + \".g.vcf.gz\"; } else { return prefix + \"output.g.vcf.gz\"; } }" . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Set up and execute manta" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "--runDir" ; cwl:valueFrom "$(runtime.outdir)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "runWorkflow.py" "-m" "local" [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-j" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/manta/bin/configManta.py" ) ; 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 "mgibio/manta_somatic-cwl:1.5.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 24000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:default "transcript" . cwl:outputSource ; 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 ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/diploidSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . rdfs:comment "Tab-delimited file containing the abundance estimates summarized in the gene level with kallisto output by Bioconductor tximport tool\n" ; rdfs:label "Gene-level abundance output by tximport with kallisto output" ; cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Coding Variant filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "--ontology" "--filter" "Consequence is coding_sequence_variant" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; 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 "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "-2" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:default "coordinate" . a cwl:CommandLineTool ; rdfs:label "Mutect2 (GATK 4)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "mutect.vcf.gz" ] ) ; cwl:baseCommand ( "/bin/bash" "Mutect2.sh" ) ; 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 "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nexport tumor_bam=\"$3\"\nexport normal_bam=\"$4\"\n\nTUMOR=`perl -e 'my $header_str = qx(samtools view -H $ENV{tumor_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the TUMOR bam.\nNORMAL=`perl -e 'my $header_str = qx(samtools view -H $ENV{normal_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the NORMAL bam.\n/gatk/gatk Mutect2 --java-options \"-Xmx20g\" -O $1 -R $2 -I $3 -tumor \"$TUMOR\" -I $4 -normal \"$NORMAL\" -L $5 #Running Mutect2.\n/gatk/gatk FilterMutectCalls -R $2 -V mutect.vcf.gz -O mutect.filtered.vcf.gz #Running FilterMutectCalls on the output vcf.\n" ; cwl:entryname "Mutect2.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ; ResourceRequirement:tmpdirMin 100000 ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "Sort VCF" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/sorted.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "SortVcf" ) ; 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:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_I/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ; sld:type cwl:File , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "RNA-Seq alignment and transcript/gene abundance 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . 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 ] . rdfs:comment "normal_name provides a string for what the WT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n" ; rdfs:label "normal_name: String specifying the name of the WT sample" ; cwl:default "normal" ; sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . rdfs:comment "Diagnosis/quality metrics summarizing the quality of sequencing read alignments from a tumor DNA sample, reported by the picard CollectAlignmentSummaryMetrics tool\n" ; rdfs:label "Sequencign alignment summary from tumor DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . 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 ] . cwl:outputBinding [ CommandOutputBinding:glob "all_D" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Picard MergeVcfs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:arguments ( "-O" "$(inputs.merged_vcf_basename).vcf.gz" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx38g" "-jar" "/gatk/gatk.jar" "MergeVcfs" ) ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "target-$(self.label)" . rdfs:comment "per_base_intervals is a list of regions (in interval_list format) over which to summarize coverage/QC at a per-base resolution." ; rdfs:label "per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . rdfs:label "Used as key for new VEP annotation" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--normalBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:CommandLineTool ; rdfs:label "cle_annotated_vcf_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ; 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:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_*.fastq" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 somatic" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "varscan_helper.sh" ) ; 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:coresMin 2 ; ResourceRequirement:ramMin 12000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\n\nset -o errexit\nset -o nounset\n\nif [ $# -lt 7 ]\nthen\n echo \"Usage: $0 [TUMOR_BAM] [NORMAL_BAM] [REFERENCE] [STRAND_FILTER] [MIN_COVERAGE] [MIN_VAR_FREQ] [P_VALUE] [roi_bed?]\"\n exit 1\nfi\n\nTUMOR_BAM=\"$1\"\nNORMAL_BAM=\"$2\"\nREFERENCE=\"$3\"\nSTRAND_FILTER=\"$4\"\nMIN_COVERAGE=\"$5\"\nMIN_VAR_FREQ=\"$6\"\nP_VALUE=\"$7\"\nOUTPUT=\"${HOME}/output\"\n\nif [ -z ${8+x} ]\nthen\n #run without ROI\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nelse\n ROI_BED=\"$8\"\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -l \"$ROI_BED\" -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nfi\n" ; cwl:entryname "varscan_helper.sh" ] ] . cwl:source . cwl:default false ; sld:type xsd:boolean . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "-x" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/combined/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . sld:type xsd:float , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "pvacseq_threads specifies the number of threads to use for parallelizing peptide-MHC binding prediction calls.\n" ; rdfs:label "pvacseq_threads: Number of threads to use for parallelizing pvacseq prediction" ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--rg" ] ; sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . sld:type xsd:int , sld:null . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:source . cwl:source . sld:type cwl:Directory , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "expand interval list regions by a given number of basepairs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)/$(inputs.interval_list.nameroot).expanded.interval_list" ] "UNIQUE=TRUE" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx3g" "-jar" "/usr/picard/picard.jar" "IntervalListTools" ) ; 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:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; 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:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:default "TUMOR" . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 8 ] ; cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . rdfs:label "sequence data with readgroup information" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "Wildtype" , "Downstream" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . rdfs:comment "reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)\nin fasta format for the entire genome. This is what reads will be aligned to.\nAppropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html\nWhen providing the reference secondary files corresponding to reference indices must be\nlocated in the same directory as the reference itself. These files can be created with\nsamtools index, bwa index, and picard CreateSequenceDictionary.\n" ; rdfs:label "reference: Reference fasta file for a desired assembly" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "an optional string to prepend to the output filename" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:valueFrom "somatic_snvs" . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:default "NORMAL" . cwl:default 400 ; sld:type xsd:int . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int . cwl:source ; cwl:valueFrom "$(self[0])" . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--reads" ] ; sld:type cwl:File . cwl:source . rdfs:comment "netmhc_stab sets an option that decides whether it will run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes.\n" ; rdfs:label "netmhc_stab: sets an option whether to run NetMHCStabPan or not" ; sld:type xsd:boolean , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.readgroup)" . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 4.1.8.1)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ; cwl:cwlVersion ; 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: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:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:docm" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--exclude-NAs" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample\n" ; rdfs:label "Sequencing per-base coverage summary at target sites from normal DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--referenceFasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a normal DNA sample, across all readGroups and per readGroup separately\n" ; rdfs:label "Sequencing quality assessment metric for normal sample genotyping" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "ALL_READS" ; sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "HaplotypeCaller (GATK4)" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "docm_haplotypeCaller.sh" ) ; 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:ramMin 9000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\n# Running haplotype caller using the newly created interval list\nif [[ \"$#\" == 5 ]];then # If normal_bam is passed.\n # explicitly capturing variables\n reference=$1\n normal_bam=$2\n tumor_bam=$3\n docm_vcf=$4\n interval_list=$5\n # Chaning the interval_list to a new docm_interval_list that spans the docm regions by 200bp\n cat $interval_list | grep '^@' > docm.interval_list # Extracting the header from the interval_list\n zcat $docm_vcf | grep ^chr | awk '{FS = \"\\t\";OFS = \"\\t\";print $1,$2-100,$2+100,\"+\",$1\"_\"$2-100\"_\"$2+100}' >> docm.interval_list # Extracting the docm regions with a 100bp flanking region on both directions\n /gatk/gatk HaplotypeCaller --java-options \"-Xmx8g\" -R $reference -I $normal_bam -I $tumor_bam --alleles $docm_vcf -L docm.interval_list --genotyping-mode GENOTYPE_GIVEN_ALLELES -O docm_raw_variants.vcf\nelse # If normal_bam is not passed\n reference=$1\n tumor_bam=$2\n docm_vcf=$3\n interval_list=$4\n # Chaning the interval_list to a new docm_interval_list that spans the docm regions by 200bp\n cat $interval_list | grep '^@' > docm.interval_list # Extracting the header from the interval_list\n zcat $docm_vcf | grep ^chr | awk '{FS = \"\\t\";OFS = \"\\t\";print $1,$2-100,$2+100,\"+\",$1\"_\"$2-100\"_\"$2+100}' >> docm.interval_list # Extracting the docm regions with a 100bp flanking region on both directions\n /gatk/gatk HaplotypeCaller --java-options \"-Xmx8g\" -R $reference -I $tumor_bam --alleles $docm_vcf -L docm.interval_list --genotyping-mode GENOTYPE_GIVEN_ALLELES -O docm_raw_variants.vcf\nfi\n" ; cwl:entryname "docm_haplotypeCaller.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0" ] . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "run vt decompose" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; 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: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:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSmallIndels.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:inputBinding [ CommandLineBinding:position -3 ] ; sld:type cwl:File . rdfs:label "List of VCF fields to annotate" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:CommandLineTool ; rdfs:label "False Positive filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . sld:type cwl:File . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Fasta file with adapters for removal that may contain N." ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . cwl:in , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "${\n if(self){\n for(var i=0; i cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--variant:strelka" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out , ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.optitype_name)_result.tsv" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:default "Wildtype" , "Downstream" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/bin/grep" "ChrID" "/dev/stdin" ) ; cwl:baseCommand ( "/bin/cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "all_region_pindel.head" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1" ; cwl:default 1 ; sld:type xsd:float . cwl:default 0 ; sld:type xsd:int , sld:null . rdfs:comment "Duplication metrics on duplicate sequencing reads from a normal DNA sample, identified by picard MarkDuplicates tool\n" ; rdfs:label "Sequencing duplicate metrics from normal DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rf'];\n } else if (inputs.strand == 'second') {\n return ['--fr'];\n } else {\n return [];\n }\n } else {\n return []\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "hla_calls/consensus_calls.txt" ; CommandOutputBinding:outputEval "$(self[0].contents.split(\",\"))" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:Directory . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "bwa-indexed reference file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:varscan" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; sld:type cwl:File . rdfs:comment "the assembly used, such as GRCh37/38, GRCm37/38" ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:in ; cwl:out ; cwl:run . rdfs:comment "normal_name provides a string for what the WT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n" ; rdfs:label "normal_name: String specifying the name of the WT sample" ; cwl:default "normal" ; sld:type xsd:string , sld:null . cwl:in , , , ; cwl:out ; cwl:run . 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:source . cwl:default 1e-01 ; sld:type xsd:float , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_2.fastq" ] ; sld:type cwl:File . cwl:valueFrom "ALL_READS" . a cwl:Workflow ; rdfs:label "Exome QC workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; 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:inputs , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "known_variants_filtered.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type cwl:Directory , xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "Consequence" , "Feature" , "HGVSp" , "SYMBOL" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; 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:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--normalBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "strelka 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . 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 ] . rdfs:comment "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" ; sld:type xsd:int . cwl:default 1 ; sld:type xsd:int . rdfs:comment "net_chop_threshold specifies the threshold to use for NetChop prediction; increasing the threshold results in better specificity, but worse sensitivity.\n" ; rdfs:label "net_chop_threshold: NetChop prediction threshold" ; sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--expn-val" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 400 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_II/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ; sld:type cwl:File , sld:null . cwl:default false ; sld:type xsd:boolean . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "combined_somatic_plus_germline.vcf" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:source . cwl:source . rdfs:comment "Reference fasta used to make the cram" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:source . sld:type cwl:File . rdfs:comment "if set to true configures manta to output assembled contig sequences in the final VCF files" ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "create BQSR table" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "BaseRecalibrator" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "BaseRecalibrator" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "BaseRecalibrator" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default "kallisto" ; sld:type xsd:string , sld:null . sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Detect Docm variants" ; 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 ] . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; 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:coresMin 8 ; ResourceRequirement:ramMin 26000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "fraction of tumor present in the normal sample (range 0 to 1) - default 0" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--normal-contamination-rate" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "pvacseq_predictions/MHC_Class_II/$(inputs.sample_name).filtered.tsv" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "Detect Variants 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:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample-name" ] ; sld:type sld:null ; 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 ] ; 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 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1" ; cwl:default 0 ; sld:type xsd:float . sld:type xsd:float , sld:null . cwl:outputSource ; 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 ] . rdfs:comment "Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)" ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; 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 ] . rdfs:comment "The effective coverage of capture products generally extends out beyond the actual regions\ntargeted. This parameter allows variants to be called in these wingspan regions, extending\nthis many base pairs from each side of the target regions.\n" ; rdfs:label "target_interval_padding: number of bp flanking each target region in which to allow variant calls" ; cwl:default 100 ; sld:type xsd:int . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . a cwl:Workflow ; rdfs:label "phase VCF" ; 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File , sld:null . cwl:default "DP" , "AD" , "GT" , "AF" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "DNA" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "reference.cnn" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "--tdna-vaf" ] ; sld:type xsd:float , sld:null . sld:type xsd:float . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . cwl:outputSource ; 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:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "phased.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if(inputs.filter_docm_variants){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; 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:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 2 ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ; sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:fields ; sld:type sld:record . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "number of chromosomes per sample" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "-ploidy" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Sanitize a VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; 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 ; 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 "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:default "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . rdfs:comment "the unaligned sequence data with readgroup information" ; sld:type . sld:type cwl:File . cwl:source . rdfs:comment "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" ; cwl:default 50 ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--maximum-transcript-support-level" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "add_gt.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "combined.vcf.gz" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka,pindel" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; 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:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ; CommandLineBinding:separate false ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . rdfs:comment "per_target_intervals list of regions (in interval_list format) over which to summarize coverage/QC at a per-target resolution." ; rdfs:label "per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:default "pvacseq" . cwl:outputSource ; sld:type cwl:File . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Each variant in this file that is also in the above file (if supplied) will be marked with a PREVIOUSLY_DISCOVERED flag in its INFO field" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:label "File to be used for annotation, include index file" ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Varscan 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:default 400 ; sld:type xsd:int . cwl:source . sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "bgzip and index VCF" ; ns1:original_cwlVersion "v1.2" ; 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:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') { \n return ['STRAND=SECOND_READ_TRANSCRIPTION_STRAND'];\n } else if (inputs.strand == 'second') {\n return ['STRAND=FIRST_READ_TRANSCRIPTION_STRAND'];\n } else {\n return ['STRAND=NONE'];\n }\n } else {\n return ['STRAND=NONE']\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "pindel v0.2.5b8" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "pindel_helper.pl" ) ; 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 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 100000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse IO::File;\n\nunless (@ARGV > 5) {\n die \"Usage: $0 normal.bam tumor.bam insert_size normal_sample_name tumor_sample_name \";\n}\n\nmy ($normal_bam, $tumor_bam, $insert_size, $normal_name, $tumor_name, @args) = @ARGV;\n\nmy $fh = IO::File->new(\"> pindel.config\");\n\n$fh->say(join(\"\\t\", $normal_bam, $insert_size, $normal_name));\n$fh->say(join(\"\\t\", $tumor_bam, $insert_size, $tumor_name));\n$fh->close;\n\nexit system(qw(/usr/bin/pindel -i pindel.config -w 30 -T 4 -o all), @args);\n" ; cwl:entryname "pindel_helper.pl" ] ] . cwl:source . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--max-uncalled" ] ; sld:type xsd:int . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "verifyBamID output files showing the sequencing depth distribution at the marker positions from Omni genotype data with a tumor DNA sample, across all readGroups and per readGroup separately\n" ; rdfs:label "Sequencing quality assessment metric for tumor sample genotyping" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_region_pindel.head" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "callers,docm" "--setKey" "null" "-o" [ cwl:valueFrom "$(runtime.outdir)/merged.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; 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:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:outputSource ; sld:type cwl:File . cwl:valueFrom "roi" . cwl:source . sld:type cwl:File . sld:type . cwl:source . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . rdfs:comment "filters to apply to reads before analysis" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--read_filter" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "The effective coverage of capture products generally extends out beyond the actual regions\ntargeted. This parameter allows variants to be called in these wingspan regions, extending\nthis many base pairs from each side of the target regions.\n" ; rdfs:label "target_interval_padding: number of bp flanking each target region in which to allow variant calls" ; cwl:default 100 ; sld:type xsd:int . cwl:source . cwl:source . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . sld:type xsd:boolean . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n inputs.field_name, \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", inputs.field_name\n ].join(\" \")\n ]\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n inputs.field_name, \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", inputs.field_name\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-e" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "the species being analyzed, such as homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--net-chop-threshold" ] ; sld:type xsd:float , sld:null . cwl:source . sld:type xsd:boolean . rdfs:comment "reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)\nin fasta format for the entire genome. This is what reads will be aligned to.\nAppropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html\nWhen providing the reference secondary files corresponding to reference indices must be\nlocated in the same directory as the reference itself. These files can be created with\nsamtools index, bwa index, and picard CreateSequenceDictionary.\n" ; rdfs:label "reference: Reference fasta file for a desired assembly" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "collect HS metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:cwlVersion ; 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 ; 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 ; 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: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 "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . rdfs:label "Use this annotation for gnomad filtering?" ; sld:type xsd:boolean , sld:null . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . rdfs:comment "normal_sequence is a yml file for which to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n" ; rdfs:label "normal_sequence: yml file specifying the location of WT sequencing data" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "verify BAM ID" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position -6 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rna-strandness RF'];\n } else if (inputs.strand == 'second') {\n return ['--rna-strandness FR'];\n } else {\n return [];\n }\n } else {\n return []\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${ \n var glob_base = \".antitarget.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n } \n return glob_base;\n} \n" ] ; sld:type cwl:File , sld:null . cwl:default false . cwl:source ; cwl:valueFrom "${ return [self]; }" . a cwl:Workflow ; rdfs:comment "somatic_exome is designed to perform processing of mutant/wildtype H.sapiens\nexome sequencing data. It features BQSR corrected alignments, 4 caller variant\ndetection, and vep style annotations. Structural variants are detected via\nmanta and cnvkit. In addition QC metrics are run, including\nsomalier concordance metrics.\n\nexample input file = analysis_workflows/example_data/somatic_exome.yaml\n" ; rdfs:label "somatic_exome: exome alignment and somatic variant detection" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , , ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "merged.bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.pdf" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:float . sld:type xsd:string . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "toggles on settings for WES" ; cwl:inputBinding [ CommandLineBinding:position -6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "concordance.somalier.pairs.tsv" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self[1])" . cwl:outputBinding [ CommandOutputBinding:glob "annotated.expression.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.expression.vcf.gz" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . rdfs:comment "Diagnosis/quality metrics showing detailed sequencing coverage per target site (optional, known variant sites of clinical significance from ClinVar for example) from a tumor DNA sample\n" ; rdfs:label "Sequencing per-base coverage summary at target sites from tumor DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--reads2" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . rdfs:label "trimming adapter file and parameters" ; sld:fields , ; sld:type sld:record . cwl:outputSource ; sld:type cwl:File . rdfs:comment "verifyBamID output files containing the contamination estimate in a normal DNA sample, across all readGroups and per readGroup separately\n" ; rdfs:label "Sequencing quality assessment metric for normal sample contamination" ; cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:source . sld:type cwl:File , sld:null . cwl:default 400 ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "somatic_llr_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "split_interval_list_helper.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "split_interval_list_helper.pl" ) ; 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:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use File::Copy;\n\nmy $retval = system('/usr/bin/java', '-jar', '/usr/picard/picard.jar', 'IntervalListTools', @ARGV);\nexit $retval if $retval != 0;\n\nmy $i = 1;\nfor(glob('*/scattered.interval_list')) {\n #create unique names and relocate all the scattered intervals to a single directory\n File::Copy::move($_, qq{$i.interval_list});\n $i++\n}\n" ; cwl:entryname "split_interval_list_helper.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use File::Copy;\n\nmy $retval = system('/usr/bin/java', '-jar', '/usr/picard/picard.jar', 'IntervalListTools', @ARGV);\nexit $retval if $retval != 0;\n\nmy $i = 1;\nfor(glob('*/scattered.interval_list')) {\n #create unique names and relocate all the scattered intervals to a single directory\n File::Copy::move($_, qq{$i.interval_list});\n $i++\n}\n" ; cwl:entryname "split_interval_list_helper.pl" ] ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "add GT tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse feature qw(say);\n\ndie(\"wrong number of arguments\") unless scalar(@ARGV) == 2;\nmy ($strelka_vcf, $outdir) = @ARGV;\n\nopen(my $strelka_vcf_fh, '-|', '/bin/gunzip', '-c', $strelka_vcf) \n or die(\"couldn't open $strelka_vcf to read\");\nopen(my $add_gt_fh, \">\", \"$outdir/add_gt.vcf\") \n or die(\"couldn't open add_gt.vcf for write\");\n\nwhile (<$strelka_vcf_fh>) {\n chomp;\n if (/^##/) {\n say $add_gt_fh $_;\n }\n elsif (/^#/) { #COLUMN HEADER\n say $add_gt_fh '##FORMAT=';\n say $add_gt_fh $_;\n }\n else {\n my @columns = split /\\t/, $_;\n my ($ref, $alt, $info) = map{$columns[$_]}(3, 4, 7);\n my @alts = split /,/, $alt;\n\n my ($n_gt, $t_gt);\n\n if (length($ref) == 1 and length($alts[0]) == 1) {\n my ($n_gt_info, $n_gt_str, $t_gt_str) = $info =~ /NT=(\\S+?);QSS.*SGT=(\\S+?)\\->(\\S+?);/;\n unshift @alts, $ref;\n\n my %ids;\n my $id = 0;\n\n for my $base (@alts) {\n $ids{$base} = $id;\n $id++;\n }\n\n $n_gt = $n_gt_info eq 'ref' ? '0/0' : parse_gt($n_gt_str, \\%ids);\n $t_gt = parse_gt($t_gt_str, \\%ids);\n }\n else {#INDEL\n my ($n_gt_info, $t_gt_info) = $info =~ /;NT=(\\S+?);.*SGT.*\\->(\\S+?);/;\n\n my %gt_info = (\n ref => '0/0',\n het => '0/1',\n hom => '1/1',\n conflict => './.',\n );\n\n $n_gt = $gt_info{$n_gt_info};\n $t_gt = $gt_info{$t_gt_info};\n }\n\n $columns[8] = 'GT:'.$columns[8];\n $columns[9] = $n_gt . ':' . $columns[9];\n $columns[10] = $t_gt . ':' . $columns[10];\n\n my $new_str = join \"\\t\", @columns;\n say $add_gt_fh $new_str;\n }\n}\n\nclose($strelka_vcf_fh);\nclose($add_gt_fh);\n\n\nsub parse_gt {\n my ($gt_str, $ids) = @_;\n my @gt_ids = map{$ids->{$_}}(split //, $gt_str);\n return join '/', sort @gt_ids;\n}\n\n#SNV example\n#1 10231 . C A . QSS_ref NT=ref;QSS=1;QSS_NT=1;SGT=AC->AC;SOMATIC;TQSS=2;TQSS_NT=2 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 32:4:8:0:0,3:28,60:0,0:0,1 84:6:69:0:7,21:71,192:0,0:0,1\n#INDEL example\n##1 965051 . ATGTGTG A . QSI_ref IC=5;IHP=2;NT=ref;QSI=1;QSI_NT=1;RC=8;RU=TG;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 8:8:6,6:0,0:2,4:10.3:0.00:0.00 18:18:8,8:5,6:5,8:21:0.25:0.00\n" ; cwl:entryname "add_strelka_gt.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . rdfs:comment "tumor_name provides a string for what the MT sample will be referred to in the various\noutputs, for exmaple the VCF files.\n" ; rdfs:label "tumor_name: String specifying the name of the MT sample" ; cwl:default "tumor" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "GTF file containing the transcripts assembled from the tumor RNA sample, created by StringTie\n" ; rdfs:label "Transcript GTF assembled from tumor RNA by StringTie" ; cwl:outputSource ; sld:type cwl:File . 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 cwl:File . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Previously discovered variants to be flagged in this pipelines's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Concordance checking between Tumor and Normal BAM" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" "concordance" ) ; cwl:baseCommand ( "/usr/bin/somalier" ) ; 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 1 ; ResourceRequirement:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "brentp/somalier:v0.1.5" ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . sld:type xsd:int . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:default 1e-01 ; sld:type xsd:float , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "net_chop_method is used to specify which NetChop prediction method to use (\"cterm\" for C term 3.0, \"20s\" for 20S 3.0).\nC-term 3.0 is trained with publicly available MHC class I ligands and the authors believe that is performs best in predicting the\nboundaries of CTL epitopes. 20S is trained with in vitro degradation data.\n" ; rdfs:label "net_chop_method: NetChop prediction method to use ('cterm' for C term 3.0, '20s' for 20S 3.0)" ; sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . a cwl:CommandLineTool ; rdfs:label "filter vcf for variants with high percentage of mapq0 reads" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/bash" "/usr/bin/mapq0_vcf_filter.sh" [ cwl:valueFrom "$(runtime.outdir)/mapq_filtered.vcf.gz" ] ) ; 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 "mgibio/mapq0-filter:v0.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:inputBinding [ CommandLineBinding:prefix "--trna-cov" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--normal-vaf" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type sld:null , cwl:File . sld:type xsd:string , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 5e-02 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 processSomatic" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; 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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Picard: BAM to FASTQ" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "F=$(runtime.outdir)/read1.fastq" ] [ cwl:valueFrom "F2=$(runtime.outdir)/read2.fastq" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/picard/picard.jar" "SamToFastq" "VALIDATION_STRINGENCY=SILENT" ) ; 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 1 ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.snvs.vcf.gz" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx8g" "LeftAlignAndTrimVariants" ) ; 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 ; 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:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "Kallisto: Quant" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "quant" "-t" "$(runtime.cores)" "-b" "100" "--fusion" "-o" "kallisto" ) ; cwl:baseCommand ( "kallisto" ) ; 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:coresMin 8 ; ResourceRequirement:ramMin 32000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "normal_sample_name is the name of the normal sample to use for phasing of germline variants.\n" ; rdfs:label "tumor_sample_name: Name of the normal sample" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type xsd:int . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:cwlVersion ; 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 ; 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:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] . sld:type xsd:int , sld:null . rdfs:comment "bqsr_intervals provides an array of genomic intervals for which to apply\nGATK base quality score recalibrations. Typically intervals are given\nfor the entire chromosome (i.e. chr1, chr2, etc.), these names should match\nthe format in the reference file.\n" ; rdfs:label "bqsr_intervals: Array of strings specifying regions for base quality score recalibration" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "tumor_sequence is a yml file for which to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n" ; rdfs:label "tumor_sequence: yml file specifying the location of MT sequencing data" ; sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--min-read-length" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; sld:type cwl:File . cwl:default true . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls" ; cwl:default true ; sld:type xsd:boolean . cwl:source ; cwl:valueFrom "base-$(self.label)" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--referenceFasta=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:default "HGVSp" , "HGVSc" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "maximum number of alternate alleles to genotype" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--max_alternate_alleles" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "The set of alleles that gatk haplotype caller will use to force-call regardless of evidence" ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; sld:type sld:null , cwl:File . cwl:source . rdfs:comment "Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a normal DNA sample\n" ; rdfs:label "Paired-end sequencing diagnosis/quality metrics from normal DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "GATK HaplotypeCaller" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "HaplotypeCaller" ) ; 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 "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source . cwl:source . cwl:default true ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-f" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default true . cwl:source . cwl:source . cwl:source . cwl:valueFrom "annotated.filtered.vcf" . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "use the binomial/llr somatic filter to weed out low confidence variants" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--overwrite" [ cwl:valueFrom "$(runtime.outdir)/somatic_llr_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/somatic_llr_filter.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/somatic-llr-filter:v0.4.3" ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "helper.txt" ; CommandOutputBinding:outputEval "$(self[0].contents.split(\" \"))" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:default false . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.tsv" ] ; sld:type cwl:File . cwl:source . cwl:valueFrom "varscan" . cwl:source . cwl:source . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:string . rdfs:comment "Sorted BAM file of sequencing read alignments by HISAT2 with duplicate reads tagged\n" ; rdfs:label "Sorted BAM from tumor RNA" ; cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "remove END INFO tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-x" "INFO/END" "-Oz" "-o" [ cwl:valueFrom "$(runtime.outdir)/pindel.noend.vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ; 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 "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GQB" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:valueFrom "ALL_READS" . cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . 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 xsd:string . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "Immunotherapy 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "Adds an INFO tag (PREVIOUSLY_DISCOVERED) flagging variants in the target vcf present in a known-variants file" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-Oz" "-o" "known_variants_filtered.vcf.gz" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ; 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:ramMin 8000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type sld:null ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n" ] ; sld:items ; sld:type sld:array ] ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n" ] ; sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumor-sample-name" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:int . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/cat" ) ; 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 "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "per_chromosome_pindel.out" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:default false . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . rdfs:comment "normal_sequence is a data structure described in sequence_data.yml used to pass information regarding\nsequencing data for single sample (i.e. fastq files). If more than one fastq file exist\nfor a sample, as in the case for multiple instrument data, the sequence tag is simply\nrepeated with the additional data (see example input file). Note that in the @RG field\nID and SM are required.\n" ; rdfs:label "normal_sequence: file specifying the location of WT sequencing data" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-bqsr" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-bqsr" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-bqsr" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-ERC" ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Read-backed phasing" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-L" [ cwl:valueFrom "$(inputs.vcf)" ] "-o" [ cwl:valueFrom "$(runtime.outdir)/phased.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "ReadBackedPhasing" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . a cwl:CommandLineTool ; rdfs:label "Custom allele frequency filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] . cwl:source . sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "annotated.filtered.final" . cwl:inputBinding [ CommandLineBinding:prefix "-c" ] ; sld:type xsd:float , sld:null . sld:type xsd:boolean , sld:null . sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "mapq_filtered.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "run pVACseq" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "$TMPDIR" ] "/tmp/pvacseq" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "export" "TMPDIR=/tmp/pvacseq" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/opt/conda/bin/pvacseq" "run" "--iedb-install-directory" "/opt/iedb" "--pass-only" [ CommandLineBinding:position 5 ; cwl:valueFrom "pvacseq_predictions" ] ) ; cwl:baseCommand ( "ln" "-s" ) ; 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 "griffithlab/pvactools:1.5.11" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.n_threads)" ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/tumorSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Create an ideogram of copy ratios on chromosomes as a PDF" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--diagram" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type cwl:File . rdfs:comment "tumor_sample_name is the name of the tumor sample being processed. When processing a multi-sample VCF the sample name must be a sample ID in the input VCF #CHROM header line.\n" ; rdfs:label "tumor_sample_name: Name of the tumor sample" ; sld:type xsd:string . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default false . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "PADDING=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "--normal-sample-name" ] ; 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 ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cns" ] ; sld:type cwl:File . cwl:source . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:prefix "--n-threads" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Minimum overlap for removal without pair overlap." ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "Known polymorphic indels recommended by GATK for a variety of\ntools including the BaseRecalibrator. This is part of the GATK resource\nbundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213\nFile should be in vcf format, and tabix indexed.\n" ; rdfs:label "bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "DNA" . cwl:in , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--fasta" ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Add snv and indel bam-readcount files to a vcf" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add bam_readcount info to vcf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; 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 ; 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: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:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:4.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type sld:null ; sld:type [ sld:symbols ; sld:type sld:enum ] . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_transcripts.gtf" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom ">" ] "helper.txt" ) ; cwl:baseCommand ( "/usr/bin/awk" "{getline; printf \"HLA-\"$2 \" HLA-\"$3 \" HLA-\"$4 \" HLA-\"$5 \" HLA-\"$6 \" HLA-\"$7}" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 2000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ; sld:type cwl:File . rdfs:comment "Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a tumor DNA sample\n" ; rdfs:label "Sequencing coverage summary of target intervals from tumor DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self)_filtered" . sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--rg-id" ] ; sld:type xsd:string . cwl:source . rdfs:comment "Use or assume a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX)" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--male-reference" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somaticSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cnr" ] ; sld:type cwl:File . cwl:source . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . rdfs:comment "toggles on or off manta settings for WES vs. WGS mode for structural variant detection" ; cwl:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:valueFrom "somatic_hc_indels" . cwl:source . cwl:default 50 ; sld:type xsd:int . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . rdfs:comment "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure." ; cwl:default 5 ; sld:type xsd:float . cwl:source . a cwl:CommandLineTool ; rdfs:label "Script to create consensus from optitype and clinical HLA typing" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "python" "hla_consensus.py" ) ; 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 "#This script produces 2-4 files depending on inputs and their contents\n#All are packaged together into a folder called hla_calls for convenience\n#optitype_calls.txt is always produced, and is essentially a copy of optitype's output\n#consensus_calls.txt is also always produced; if no clinical calls are provided, this\n#file is identical to optitype_calls.txt. If clinical calls are provided, they are\n#reproduced in clinical_calls.txt. If the clinical calls exactly match the optitype calls*, \n#all 3 files described so far will contain the same information, but are not guaranteed to\n#be exactly the same (text ordering may differ, depending on the order calls are given in the input). \n#If the clinical calls and optitype calls do not match, mismatched_calls.txt is then produced;\n#each line represents a gene. See below (section 'write out call files') for more mismatch details.\n#NOTE: optitype only produces MHC class I calls\n\n#optitype input format (should be automatic):\n#HLA-X*01:02\n#clinical input format (each element of the input array):\n#note that each individual call should be a single element of the array\n#a group of alleles separated by '/' indicates an uncertain call and the\n#its possible alleles; the entire group comprises a single element of the array\n#HLA-X*01:02[/HLA-X...]\n#NOTE: hla calls may have up to 4 ':' separated fields; however, this tool strips all\n# but the first 2, because the downstream tools only support 2 fields\n# eg HLA-X*01:02:03:04, while valid, will be treated as HLA-X*01:02\n\nimport sys, os\nfrom collections import defaultdict\n\n####################################\n### helper methods for later use ###\n####################################\n\n#helper method that takes in the decomposed version of an hla\n#string and returns the full delimited string\ndef build_hla_str(gene, allele_group, spec_allele):\n return gene + \"*\" + allele_group + \":\" + spec_allele\n\n#helper method that takes in a full hla string, like HLA-X*01:02:03:04,\n#and splits it into the gene name (HLA-X), allele group (01), and the\n#specific allele (02), dropping any fields beyond this, because downstream\n#tool do not support these fields\ndef split_hla_str(full_hla_str):\n gene_name, raw_allele_fields = full_hla_str.split('*')\n split_allele_fields = raw_allele_fields.split(\":\")\n allele_group_name = split_allele_fields[0]\n specific_allele_name = split_allele_fields[1]\n return (gene_name, allele_group_name, specific_allele_name)\n\n#helper method that creates a mismatch file only if any have been found in the tree,\n#and inserts a header upon initially creating the file. Params:\n#previously_written- true if the file has already been created; used control header creation\n#mismatches- dictionary with sources as keys and a list of alleles called only by that\n# source as values\n#returns true if the file was or has ever been written to, false otherwise\ndef write_mismatch(previously_written, mismatches):\n if (not(mismatches['optitype'] or mismatches['clinical'])):\n #In this case, both arrays are empty, so there's no mismatch to write\n #function has not changed the file state, so return the unmodified flag\n return previously_written\n\n with open(\"hla_calls/mismatched_calls.txt\", \"a\") as m_c:\n if not previously_written:\n #add header if this is the first time writing to the file\n m_c.write(\"optitype_calls\\tclinical_calls\\n\")\n #write the mismatches to the file\n m_c.write( \",\".join(mismatches['optitype']) + \"\\t\" + \",\".join(mismatches['clinical']) + \"\\n\" )\n\n return True\n\n########################################\n### parse args from the command line ###\n########################################\n\nclinical_exists = len(sys.argv) > 2 \n\noptitype_calls = sys.argv[1].split(\",\")\n\nif clinical_exists:\n raw_clinical_i_calls = sys.argv[2].split(\",\") #MHC Class I clinical typing results\n raw_clinical_ii_calls = sys.argv[3].split(\",\") #MHC Class II clinical typing results\n #Each clinical call may be a single high confidence call,\n #or a list of uncertain calls separated by slashes\n hc_clinical_calls = []\n u_clinical_calls = []\n for call in raw_clinical_i_calls:\n if \"/\" in call:\n u_clinical_calls.append(call)\n else:\n hc_clinical_calls.append(call)\n\n################################################################\n### Load HLA types into data structure for consensus calling ###\n################################################################\n\n#Create a basic tree out of dictionaries to hold the data from all callers;\n#top level keys will be genes, pointing to a nested dictionary with\n#allele groups as keys, pointing to a final dictionary with specific alleles\n#as keys and a set containing call sources as values\n# ex: optitype calls HLA-A*01:02 -> {HLA-A: {01: {02: {optitype}}}}\n\n#defaultdict constructor requires a callable; however, it returns an object\n#lambdas create a callable that allows for nested defaultdicts\nhla_calls = defaultdict( lambda: defaultdict( lambda: defaultdict(set) ) )\n\nfor call in optitype_calls:\n gene, allele_group, spec_allele = split_hla_str(call)\n\n #records this call in the tree and tags it as coming from optitype\n #the tag is added to a set, so any duplicates (such as from an individual homozygous\n #for a given gene) are collapsed into a single entry\n hla_calls[gene][allele_group][spec_allele].add('optitype')\n\nif clinical_exists:\n for call in hc_clinical_calls:\n gene, allele_group, spec_allele = split_hla_str(call)\n\n #Case 1: this $call was also called by optitype, so add to the \n #record indicating that clinical data supports this call\n #Case 2: this call is unique to the clinical data; create a record \n #and indicate that only clinical data supports this call\n hla_calls[gene][allele_group][spec_allele].add('clinical')\n\n for multi_call in u_clinical_calls:\n calls = multi_call.split(\"/\")\n multi_consensus = set()\n for call in calls:\n gene, allele_group, spec_allele = split_hla_str(call)\n\n #check if this call already exists in the tree, which will be treated as\n #evidence that this call is the correct call out of the current group of\n #uncertain calls ($multi_call)\n\n #TODO this may be biased towards creating a homozygous consensus:\n #since high confidence clinical calls are evaluated before this, one of \n #these calls could be used as evidence when resolving the uncertain call\n #using the current method. Is this desirable? Should we only use optitype calls\n #when resolving uncertain clinical calls?\n #Example: clinical calls 01:02 and 01:02/01:03/01:04\n if hla_calls[gene][allele_group][spec_allele]:\n #add as a tuple to avoid re-splitting later\n multi_consensus.add( (gene, allele_group, spec_allele) )\n\n #if one and only one of the calls from the uncertain group was already in the tree,\n #that is treated as evidence that this particular call was the correct one. It will\n #be accepted and entered into the tree, while the other calls will be discarded\n if len(multi_consensus) == 1:\n accpt_call = multi_consensus.pop()\n hla_calls[accpt_call[0]][accpt_call[1]][accpt_call[2]].add('clinical')\n #otherwise, all uncertain calls from the group will be added to the tree; this means\n #they will be added to the consensus superset (since their validity cannot be disproven),\n #and also used to construct the mismatch file\n else:\n for call in calls:\n gene, allele_group, spec_allele = split_hla_str(call)\n hla_calls[gene][allele_group][spec_allele].add('clinical')\n\n##############################################\n### write out caller files for convenience ###\n##############################################\n\nos.mkdir(\"hla_calls\")\n\n#Create an exact copy of optitype calls, to be bundled with other relevant\n#files for convenience/later review. Always generated,\nwith open(\"hla_calls/optitype_calls.txt\", \"w\") as o_c:\n o_c.write( \",\".join(optitype_calls) )\n\n#Create an exact copy of clinical calls, if they exist, to be bundled with \n#other relevant files for convenience/later review.\nif clinical_exists:\n with open(\"hla_calls/clinical_calls.txt\", \"w\") as c_c:\n c_c.write( \",\".join(raw_clinical_i_calls + raw_clinical_ii_calls) )\n\n#########################################################\n### Generate consensus (superset if callers disagree) ###\n#########################################################\n\n#A consensus file is always generated to be passed on to pvacseq. If there are\n#no clinical calls, this file is the same as optitype_calls.txt. If there are, walk\n#through the tree and emit everything present as the consensus. If there is a true\n#consensus, each class I gene (corresponding to the top level keys of the tree) will have\n#at most 2 leaves (1 in the case of a homozygote, or in the rare case that both optitype\n#and clinical data only called one allele for this gene), where each leaf represents\n#a specific allele call supported by both sources. If there is no true consensus, there\n#may be more than 2 leaves per class I gene, and individual leaves may only be supported by\n#1 of the 2 sources. These leaves will still be added to the consensus to form a superset,\n#since there is not enough evidence to discard them, but they will also be added to a\n#mismatch file, which presents side by side lists of the differing alleles called by each\n#source, with one gene per line. Note that optitype only makes class I predictions, so any\n#class II predictions from the clinical data are always added to the consensus and never\n#to the mismatch file\nif not clinical_exists:\n with open(\"hla_calls/consensus_calls.txt\", \"w\") as c_c:\n c_c.write( \",\".join(optitype_calls) )\nelse:\n consensus_calls = []\n consensus_calls.extend(raw_clinical_ii_calls)\n mismatch_written = False\n for gene in hla_calls:\n mismatches = {'optitype': [], 'clinical': []}\n for allele_group in hla_calls[gene]:\n for spec_allele in hla_calls[gene][allele_group]:\n callers = hla_calls[gene][allele_group][spec_allele]\n\n #if any uncertain calls were resolved to a single call based on prior\n #evidence, the discarded calls will have been visited but not tagged,\n #resulting in leaves with empty sets; these can be ignored\n if callers:\n #there are now only 3 possibilities for the contents of $callers:\n #[optitype, clinical], [optitype], [clinical]\n #all will be added to the consensus, possibly creating a superset\n #those with only 1 caller represent mismatches between the 2\n consensus_calls.append( build_hla_str(gene, allele_group, spec_allele) )\n if len(callers) == 1:\n mismatches[callers.pop()].append( build_hla_str(gene, allele_group, spec_allele) )\n\n mismatch_written = write_mismatch(mismatch_written, mismatches)\n\n with open(\"hla_calls/consensus_calls.txt\", \"w\") as c_c:\n c_c.write( \",\".join(consensus_calls) )\n" ; cwl:entryname "hla_consensus.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "python:3.7.4-slim-buster" ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:string . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "exome alignment and germline variant detection" ; 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:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:Directory . sld:type xsd:int . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . rdfs:comment "Previously generated reference.cnn file" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--reference" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--netmhc-stab" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] ; sld:type [ sld:items ; sld:type sld:array ] . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default "RNA" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "sorted.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:source . cwl:source . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--cache_version" ] ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "concordance.somalier.samples.tsv" ] ; sld:type cwl:File . cwl:source . rdfs:comment "target_intervals is an interval_list corresponding to the targets for the capture reagent.\nBed files with this information can be converted to interval_lists with Picard BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n" ; rdfs:label "target_intervals: interval_list file of targets used in the sequencing experiment" ; sld:type cwl:File . rdfs:comment "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:int , sld:null . rdfs:comment "Diagnosis/quality metrics showing detailed sequencing coverage per target interval (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample\n" ; rdfs:label "Sequencing per-target coverage summary of target intervals from normal DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type sld:null ; 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:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "output.indel.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . rdfs:comment "bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.\nThese are essentially coordinates for regions you were able to design probes for in the reagent.\nTypically the reagent provider has this information available in bed format and it can be\nconverted to an interval_list with Picard BedToIntervalList. AstraZeneca also maintains a repo\nof baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data\n" ; rdfs:label "bait_intervals: interval_list file of baits used in the sequencing experiment" ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "Raw sequence data to BQSR" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; 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:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] . rdfs:comment "Diagnosis/quality metrics including the insert size distribution and read orientation of the paired-end libraries from a tumor DNA sample\n" ; rdfs:label "Paired-end sequencing diagnosis/quality metrics from tumor DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pindel.out.vcf" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type cwl:File . cwl:source . cwl:default false ; sld:type xsd:boolean . cwl:source . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--variant:pindel" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:mutect" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source , , , , . cwl:source . sld:type sld:null ; 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 . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "SEQUENCE_DICTIONARY=" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*.interval.bed" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumorBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--minimum_depth" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; sld:type cwl:File . rdfs:comment "Diagnosis/quality metrics for sequencing coverage for target intervals (optional, 59 genes recommended by ACMG for clinical exome and genome sequencing for example) from a normal DNA sample\n" ; rdfs:label "Sequencing coverage summary of target intervals from normal DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-f" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-V" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--targets" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Regions of accessible sequence on chromosomes (.bed), as output by the 'access' command" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--access" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).targetcoverage.cnn" ] ; sld:type cwl:File . cwl:source . sld:type sld:null ; sld:type [ sld:symbols ; sld:type sld:enum ] . a cwl:CommandLineTool ; rdfs:label "apply BQSR" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "--static-quantized-quals" "10" "--static-quantized-quals" "20" "--static-quantized-quals" "30" ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "--static-quantized-quals" "10" "--static-quantized-quals" "20" "--static-quantized-quals" "30" ) ; cwl:arguments ( "-O" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "--static-quantized-quals" "10" "--static-quantized-quals" "20" "--static-quantized-quals" "30" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "ApplyBQSR" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "ApplyBQSR" ) ; cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "ApplyBQSR" ) ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1" ] . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapters" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:valueFrom "strelka" . cwl:source , . rdfs:comment "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" ; sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.nameroot)_annotated.vcf" ] ) ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.nameroot)_annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -8 ] ; cwl:inputBinding [ CommandLineBinding:position -8 ] ; cwl:inputBinding [ CommandLineBinding:position -8 ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$((self.secondaryFiles !== undefined) ? self.secondaryFiles.find(function(x) { return x.nameext === \".dict\" }) : self.replace(/.fa$/,\".dict\") )" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "depth_filtered.vcf" ] ; sld:type cwl:File . sld:type xsd:float . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:cwlVersion ; 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:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nRUN_TRIMMING=\"false\"\n\nwhile getopts \"b:?1:?2:?g:r:n:t:?o:?\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n t)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTERS=\"$OPTARG\"\n ;;\n o)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTER_MIN_OVERLAP=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads \"$FASTQ1\" --reads2 \"$FASTQ2\" --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \\\n | /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads - --interleaved --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nRUN_TRIMMING=\"false\"\n\nwhile getopts \"b:?1:?2:?g:r:n:t:?o:?\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n t)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTERS=\"$OPTARG\"\n ;;\n o)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTER_MIN_OVERLAP=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads \"$FASTQ1\" --reads2 \"$FASTQ2\" --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \\\n | /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads - --interleaved --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nRUN_TRIMMING=\"false\"\n\nwhile getopts \"b:?1:?2:?g:r:n:t:?o:?\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n t)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTERS=\"$OPTARG\"\n ;;\n o)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTER_MIN_OVERLAP=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads \"$FASTQ1\" --reads2 \"$FASTQ2\" --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \\\n | /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads - --interleaved --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:stdout "refAlign.bam" . cwl:source . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int . rdfs:comment "The name of a genotype field to include in the output table" ; cwl:default "AD" , "GT" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:valueFrom "mutect" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.indels.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ cwl:valueFrom "$( ['-t', self.adapters.path, '-o', self.min_overlap] )" ] ; cwl:inputBinding [ cwl:valueFrom "$( ['-t', self.adapters.path, '-o', self.min_overlap] )" ] ; cwl:inputBinding [ cwl:valueFrom "$( ['-t', self.adapters.path, '-o', self.min_overlap] )" ] ; sld:type , sld:null . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--tdna-cov" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Per-region pindel" ; 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:outputBinding [ CommandOutputBinding:glob "docm_filtered_variants.vcf" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:default 5e-02 ; sld:type xsd:float , sld:null . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "filter" ] ; sld:type xsd:boolean . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:fields , , , , , ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools index cram" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "tumor cellularity fraction (range 0 to 1) - default 1" ; cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--tumor-purity" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 3 ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self).bam" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out , ; cwl:run . cwl:default "variants" ; sld:type xsd:string , sld:null . sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Diagnosis/quality metrics for sequencing coverage at target sites (optional, known variant sites of clinical significance from ClinVar for example) from a normal DNA sample\n" ; rdfs:label "Sequencing coverage summary at target sites from normal DNA" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".target.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . cwl:source . cwl:valueFrom "annotated.filtered.tsv" . cwl:source . cwl:default true . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-contamination" ] ; sld:type xsd:string , sld:null . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; 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 [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:Directory . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-j" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--adapter-min-overlap" ] ; sld:type xsd:int . cwl:default 400 ; sld:type xsd:int . cwl:source . cwl:default false . a cwl:CommandLineTool ; rdfs:label "Samtools: merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:cwlVersion ; 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:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "Trim FASTQ (flexbar)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--target" [ cwl:valueFrom "$(runtime.outdir)/trimmed_read" ] "--threads" [ cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/flexbar/flexbar" ) ; 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:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bisulfite:v1.4" ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:source . rdfs:comment "Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls" ; cwl:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "docm_raw_variants.vcf" ] ; sld:type cwl:File . cwl:outputSource ; 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 xsd:string . cwl:source . sld:type xsd:float , sld:null . sld:type xsd:string . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type cwl:File . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . a cwl:Workflow ; rdfs:label "scatter GATK HaplotypeCaller over intervals" ; 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:InlineJavascriptRequirement ] . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "select only a certain type of variants" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-select-type" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-V" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "${\n if(self){\n for(var i=0; i cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "Normal samples (.bam) used to construct the pooled, paired, or flat reference. If this option is used but no filenames are given, a 'flat' reference will be built. Otherwise, all filenames following this option will be used." ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--drop-low-coverage" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:source . 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:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-D" ] ; sld:type cwl:File , xsd:string , sld:null . rdfs:comment "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure." ; cwl:default 5 ; sld:type xsd:float . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "vcf merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.3.1" ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:default "HGVSp" , "HGVSc" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type , . rdfs:comment "Duplication metrics on duplicate sequencing reads from a tumor DNA sample, identified by picard MarkDuplicates tool\n" ; rdfs:label "Sequencing duplicate metrics from tumor DNA" ; cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "A prefix that will be used to name all files produced by the script" ; cwl:default "optitype" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "if set to true, vep only returns consequences that fall in the coding regions of transcripts" ; sld:type xsd:boolean , sld:null . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . rdfs:comment "configures how vep will annotate genomic features that each variant overlaps; for a detailed description of each option see https://useast.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick_allele_gene_eg" ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Tab-delimited file containing gene abundances in FPKM and TPM, created by StringTie\n" ; rdfs:label "Gene abundance table from tumor RNA by StringTie" ; cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "TUMOR" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "A vcf of previously discovered variants to be marked in the second input vcf; if not provided, this tool does nothing but rename the second input vcf" ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n return [ '-a', self.path, '-m', 'PREVIOUSLY_DISCOVERED' ];\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-a" ] ; sld:type sld:null ; sld:type [ sld:symbols ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.h5" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_INV" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--normal-sample-name" ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "Previously discovered variants to be flagged in this workflow's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:default "output.g.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "-O" ] ; sld:type xsd:string . cwl:source .