#!/usr/bin/env cwl-runner cwlVersion: v1.0 doc: | This is a subworkflow - this is not meant to be run as a stand-alone workflow! requirements: - class: SchemaDefRequirement types: - $import: TumourType.yaml - class: ScatterFeatureRequirement - class: StepInputExpressionRequirement - class: MultipleInputFeatureRequirement - class: InlineJavascriptRequirement expressionLib: - { $include: oxog_util.js } - class: SubworkflowFeatureRequirement class: Workflow outputs: oxogVCF: outputSource: sub_run_oxog/oxogVCF type: File[] oxogTBI: outputSource: sub_run_oxog/oxogTBI type: File[] inputs: vcfsForOxoG: type: File[] inputFileDirectory: type: Directory in_data: type: "TumourType.yaml#TumourType" refDataDir: type: Directory steps: sub_run_oxog: run: oxog.cwl in: inputFileDirectory: inputFileDirectory tumourID: source: [in_data] valueFrom: | ${ return self.tumourId } tumourBamFilename: source: [inputFileDirectory, in_data] valueFrom: | ${ return { "class":"File", "location": self[0].location + "/" + self[1].bamFileName } } refDataDir: refDataDir oxoQScore: source: [in_data] valueFrom: | ${ return self.oxoQScore } vcfNames: source: [in_data, vcfsForOxoG] valueFrom: | ${ return createArrayOfFilesForOxoG(self[0], self[1]) } out: [oxogVCF, oxogTBI]