@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix dct: .
@prefix rdf: .
@prefix cwl: .
@prefix ExpressionTool: .
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:fields , , , ;
sld:type sld:record .
cwl:outputBinding [ CommandOutputBinding:glob
"*.normalized.vcf.gz" ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:comment "This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.\n" ;
ns2:original_cwlVersion "v1.0" ;
dct:creator [ ns1:mbox "solomon.shorser@oicr.on.ca" ;
ns1:name "Solomon Shorser"
] ;
Workflow:steps , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"\n/**\n * Filters an array of files. Returns an array that only contains files that contain \"indel\" in their name.\n * @param inArr - the array.\n * @return a filtered array - it will only contain files whose names contain the string \"indel\".\n */\nfunction filterForIndels(inArr)\n{\n\tvar arr = [];\n\tfor (var i = 0; i < inArr.length ; i++)\n\t{\n\t\tif (inArr[i].basename.indexOf(\"indel\") >= 0)\n\t\t{\n\t\t\tarr.push(inArr[i]);\n\t\t}\n\t}\n\treturn arr;\n}\n\n/**\n * This function will filter an array of files and select only files that match\n * workflowName and vcfType.\n * @param workflowName - the name of the workflow to filter for.\n * @param vcfType - the type of VCF (snv, indel, etc...)\n * @param inArr - an array of files (File[]) to search through.\n * @return an array that has been filtered.\n */\nfunction filterFor(workflowName, vcfType, inArr)\n{\n\tvar arr = [];\n\tfor (var i = 0; i < inArr.length; i++)\n\t{\n\t\tif (typeof(inArr[i]) == \"string\") //(\"class\" in inArr[i] && inArr[i].class == \"File\")\n\t\t{\n\t\t\tif (inArr[i].indexOf(workflowName) >= 0 && inArr[i].indexOf(vcfType) >= 0)\n\t\t\t{\n\t\t\t\tarr.push(inArr[i])\n\t\t\t}\n\t\t}\n\t\telse\n\t\t{\n\t\t\tif (\"class\" in inArr[i] && inArr[i].class == \"File\")\n\t\t\t{\n\t\t\t\tif (inArr[i].basename.indexOf(workflowName) >= 0 && inArr[i].basename.indexOf(vcfType) >= 0)\n\t\t\t\t{\n\t\t\t\t\tarr.push(inArr[i])\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn arr;\n}\n"
] .
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "This tool will pass-filter a VCF.\n" ;
rdfs:label "pass-filter" ;
ns2:original_cwlVersion "v1.0" ;
dct:creator [ ns1:mbox "solomon.shorser@oicr.on.ca" ;
ns1:name "Solomon Shorser"
] ;
cwl:arguments ( "$(inputs.vcfdir.path)" "$(inputs.filesToFilter)" ) ;
cwl:baseCommand ( "/opt/oxog_scripts/pass_filter.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/pancancer/pcawg-oxog-tools"
] .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
rdfs:comment "Normalize the INDEL VCFs." ;
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
rdfs:comment "Filters the input list and selects the INDEL VCFs." ;
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "The name of the output directory" ;
sld:type xsd:string .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "Clean the VCFs." ;
cwl:in ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
a cwl:CommandLineTool ;
rdfs:comment "This tool will normalize an INDEL VCF using bcf-tools norm.\n" ;
rdfs:label "normalize" ;
ns2:original_cwlVersion "v1.0" ;
dct:creator [ ns1:mbox "solomon.shorser@oicr.on.ca" ;
ns1:name "Solomon Shorser"
] ;
cwl:baseCommand ( "/opt/oxog_scripts/normalize.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/pancancer/pcawg-oxog-tools"
] .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "The directory where the files are" ;
sld:type cwl:Directory .
rdfs:comment "The files to process" ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:ExpressionTool ;
ExpressionTool:expression "$({ out_vcf: filterForIndels(inputs.in_vcf) })\n" ;
cwl:inputs ;
cwl:outputs .
rdfs:comment "Reference file, used for normalized INDELs" ;
sld:type cwl:File .
sld:type .
cwl:source .
a cwl:ExpressionTool ;
ExpressionTool:expression "$(\n {output_record: {\n \"normalizedVcfs\": inputs.normalizedVcfs\n }}\n)\n" ;
cwl:inputs ;
cwl:outputs .
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "The names of the files that will actually be filtered" ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Filter out non-PASS lines from the VCFs in filesToProcess." ;
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source ;
cwl:valueFrom "${\n var VCFs = []\n for (var i in self)\n {\n if (self[i].toLowerCase().indexOf(\"muse\") == -1)\n {\n VCFs.push(self[i]);\n }\n }\n return VCFs;\n}\n" .
rdfs:comment "The directory containing the files" ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"*.pass-filtered.vcf.gz" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "This tool will clean a VCF for use in the OxoG workflow.\n" ;
rdfs:label "clean-vcf" ;
ns2:original_cwlVersion "v1.0" ;
dct:creator [ ns1:mbox "solomon.shorser@oicr.on.ca" ;
ns1:name "Solomon Shorser"
] ;
cwl:baseCommand ( "/opt/oxog_scripts/clean_vcf.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/pancancer/pcawg-oxog-tools"
] .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.cleaned.vcf" ] ;
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type .