@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix EnvVarRequirement: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix InlineJavascriptRequirement: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix EnvironmentDef: . @prefix cwl: . @prefix ResourceRequirement: . @prefix ExpressionTool: . cwl:default ; sld:type cwl:File . rdfs:comment "Reference fasta file" ; cwl:inputBinding [ CommandLineBinding:position 21 ; CommandLineBinding:prefix "--reference_fasta" ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "aliquotmaf" "VcfToAliquotMaf" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/aliquot-maf-tools:{{ aliquot_maf_tools }}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${\n var listing = []\n listing.push(inputs.reference_fasta)\n listing.push(inputs.reference_fasta_index)\n return listing\n}\n" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function lookup_optional_file(opt_obj, key) {\n var res = [];\n\n for (var i=0; i sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Optional hotspot TSV" ; cwl:inputBinding [ CommandLineBinding:position 26 ; CommandLineBinding:prefix "--hotspot_tsv" ] ; sld:type cwl:File , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:default "upload" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:source . cwl:default "gdc-2.0.0-aliquot" ; sld:type xsd:string . sld:type xsd:string . cwl:default "NORMAL" ; sld:type xsd:string , sld:null . sld:type xsd:string . rdfs:comment "Reference fasta fai file" ; cwl:inputBinding [ CommandLineBinding:position 22 ; CommandLineBinding:prefix "--reference_fasta_index" ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:source . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; cwl:inputBinding [ CommandLineBinding:position 99 ; CommandLineBinding:prefix "--dir_path" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 99 ] ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . sld:fields , ; sld:type sld:record . sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:type . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string . sld:type xsd:string . rdfs:comment "The sequencing center" ; cwl:inputBinding [ CommandLineBinding:position 16 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--maf_center" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default 5 ; sld:type xsd:int . sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "The UUID of the src VCF file" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--src_vcf_uuid" ] ; sld:type xsd:string . rdfs:comment "basename of output MAF file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--output_maf" ] ; sld:type xsd:string . cwl:default "download" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . sld:type xsd:string . cwl:source . a cwl:Workflow ; rdfs:comment "This copy is for use with the new merged panel of normals" ; 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:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function lookup_optional_file(opt_obj, key) {\n var res = [];\n\n for (var i=0; i cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.parent_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.parent_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.parent_file.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--upload-bucket" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self + '.aliquot.maf.gz')" . cwl:source . sld:type xsd:string . cwl:source . cwl:source . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var single_output = [];\n var indexed_output = [];\n var singles = [\n \"custom_enst_uuid\", \"dbsnp_priority_db_uuid\", \"hotspot_tsv_uuid\", \"gdc_blacklist_uuid\"\n ];\n var pairs = [\n [\"cosmic_vcf_uuid\", \"cosmic_vcf_index_uuid\"],\n [\"gdc_pon_vcf_uuid\", \"gdc_pon_vcf_index_uuid\"],\n [\"nonexonic_intervals_uuid\", \"nonexonic_intervals_index_uuid\"],\n ];\n\n for(var i = 0; i ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.index_uuid)" . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Name of the normal sample in the VCF, typically 'NORMAL'" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--normal_vcf_id" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type xsd:string . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n return {\"output\": {\"key\": inputs.file_key, \"file\": inputs.main_file}};\n }\n" ; 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:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . cwl:default ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/bio_client.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 "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax 1 ; ResourceRequirement:outdirMin 1 ; ResourceRequirement:ramMax 1000 ; ResourceRequirement:ramMin 1000 ; ResourceRequirement:tmpdirMax 1 ; ResourceRequirement:tmpdirMin 1 ] . cwl:source . sld:type xsd:string , sld:null . rdfs:comment "Tumor sample aliquot submitter ID" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--tumor_submitter_id" ] ; sld:type xsd:string . cwl:source . cwl:source . rdfs:comment "Normal sample aliquot submitter ID" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--normal_submitter_id" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*" ] ; sld:type cwl:File . rdfs:comment "Tumor sample bam UUID" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--tumor_bam_uuid" ] ; sld:type xsd:string . cwl:source . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"gdc_blacklist_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:default 7 ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . sld:type . cwl:source . cwl:source . sld:type xsd:string . cwl:default 1e-03 ; cwl:inputBinding [ CommandLineBinding:position 34 ; CommandLineBinding:prefix "--gnomad_af_cutoff" ] ; sld:type xsd:float . sld:type xsd:string . rdfs:comment "The file containing the blacklist tags and tumor aliquot uuids to apply them to." ; cwl:inputBinding [ CommandLineBinding:position 28 ; CommandLineBinding:prefix "--gdc_blacklist" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "The tabix-indexed panel of normals VCF for applying the gdc pon filter" ; cwl:inputBinding [ CommandLineBinding:position 30 ; CommandLineBinding:prefix "--gdc_pon_vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Optional custom ENST overrides" ; cwl:inputBinding [ CommandLineBinding:position 19 ; CommandLineBinding:prefix "--custom_enst" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:default "TUMOR" ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:source . sld:type xsd:string , sld:null . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string , sld:null . rdfs:comment "Effect priority JSON" ; cwl:inputBinding [ CommandLineBinding:position 18 ; CommandLineBinding:prefix "--effect_priority_file" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "Flag variants outside of this tabix-indexed bed file as NonExonic" ; cwl:inputBinding [ CommandLineBinding:position 31 ; CommandLineBinding:prefix "--nonexonic_intervals" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:default 1 ; sld:type xsd:long . rdfs:comment "Flag variants outside of these tabix-indexed bed files as off_target. Use one or more times." ; cwl:inputBinding [ CommandLineBinding:position 32 ] ; cwl:secondaryFiles [] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--target_intervals" ] ; sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . sld:type xsd:string . a cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "Normal sample bam UUID" ; cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "--normal_bam_uuid" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:fields , , ; sld:type sld:record . cwl:source . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var output_value = JSON.parse(inputs.input.contents)[inputs.key];\n return {'output': output_value};\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source ; cwl:valueFrom "$(self.uuid)" . cwl:source . sld:type xsd:string . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . rdfs:comment "the schema to use for the maf" ; cwl:default "gdc-2.0.0-aliquot" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , ; cwl:run . cwl:source . rdfs:comment "Name of the caller used to detect mutations" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--caller_id" ] ; sld:type xsd:string . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . sld:type xsd:string . sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.key)" . rdfs:comment "The sequencer used" ; cwl:inputBinding [ CommandLineBinding:position 15 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--sequencer" ] ; sld:items xsd:string ; sld:type sld:array ] . sld:type . cwl:source . sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.uuid)" . sld:type xsd:string , sld:null . sld:fields , ; sld:type sld:record . sld:type xsd:string . rdfs:comment "Biotype priority JSON" ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "--biotype_priority_file" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"target_intervals\");\n return f.length == 0 ? null : f;\n }\n" . cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var output = [];\n\n for (var i = 0; i < inputs.input_a.length; i++) {\n var curr = inputs.input_a[i];\n output.push(curr);\n }\n\n for (var i = 0; i < inputs.input_b.length; i++) {\n var curr = inputs.input_b[i];\n output.push(curr);\n }\n\n return {'output': output}\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . sld:type xsd:string , sld:null . sld:type xsd:string . rdfs:comment "Tabix-indexed VEP annotated VCF file" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--input_vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . 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 cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$([self])" . rdfs:comment "Name of the tumor sample in the VCF, typically 'TUMOR'" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--tumor_vcf_id" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 33 ; CommandLineBinding:prefix "--gnomad_noncancer_vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--upload_key" ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"cosmic_vcf_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . cwl:outputBinding [ CommandOutputBinding:glob "*_upload.json" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"hotspot_tsv_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:type cwl:File . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var exp = inputs.experimental_strategy.toLowerCase().replace(/[\\-]/g, \" \").replace(/\\s+/g, '_');\n var pid = inputs.project_id ? inputs.project_id + '.': '';\n var cid = inputs.caller_id ? '.' + inputs.caller_id.replace(/[\\-]/g, \" \").replace(/\\s+/g, '_') : '';\n var pfx = pid + inputs.job_uuid + '.' + exp + cid; \n return {'output': pfx};\n }\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string , sld:null . sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"gdc_pon_vcf_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--config-file" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"custom_enst_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . cwl:in , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self.key)" . cwl:source . sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type xsd:string . sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; cwl:inputBinding [ CommandLineBinding:position 98 ] ; sld:type xsd:string . sld:type xsd:string , sld:null . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ; cwl: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 ; 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 ; 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: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 "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ; EnvironmentDef:envValue "$(inputs.cert.path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:coresMin 1 ; ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:ramMax 2000 ; ResourceRequirement:ramMin 2000 ; ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ; ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))" ] . cwl:source . rdfs:comment "Number of BP to add both upstream and downstream from variant for reference context" ; cwl:default 5 ; cwl:inputBinding [ CommandLineBinding:position 23 ; CommandLineBinding:prefix "--reference_context_size" ] ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:source . cwl:source , ; cwl:valueFrom "$(self[0] + '/' + self[1].basename)" . rdfs:comment "Tumor sample aliquot UUID" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--tumor_aliquot_uuid" ] ; sld:type xsd:string . cwl:default "did" . rdfs:comment "Is this a tumor-only VCF?" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumor_only" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type . sld:type xsd:string , sld:null . rdfs:comment "Normal sample aliquot UUID" ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "--normal_aliquot_uuid" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "Flag variants where normal depth is <= INT as ndp [7]." ; cwl:inputBinding [ CommandLineBinding:position 29 ; CommandLineBinding:prefix "--min_n_depth" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type xsd:string . cwl:source . rdfs:comment "Optional COSMIC VCF for annotating" ; cwl:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "--cosmic_vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "true" ) ; cwl:baseCommand ( "true" ) ; cwl:baseCommand ( "true" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.children)" , "$(inputs.parent_file)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.children)" , "$(inputs.parent_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "{{ docker_repo }}/bio-alpine:{{ bio_alpine }}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.children)" , "$(inputs.parent_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "JSON file used to look up entrez IDs given HGNC symbols or gencode IDs" ; cwl:inputBinding [ CommandLineBinding:position 35 ; CommandLineBinding:prefix "--entrez_gene_id_json" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:default 1e-03 ; sld:type xsd:float , sld:null . sld:type xsd:string . cwl:source . cwl:source . cwl:source . sld:type xsd:string . cwl:source ; cwl:valueFrom "${\n var f = lookup_optional_file(self, \"nonexonic_intervals_uuid\");\n return f.length == 0 ? null : f[0];\n }\n" . rdfs:comment "Sample case UUID" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--case_uuid" ] ; sld:type xsd:string . cwl:source .