#!/usr/bin/env cwl-runner cwlVersion: v1.0 doc: | This is a subworkflow of the main oxog_varbam_annotat_wf workflow - 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: varbam_util.js } - class: SubworkflowFeatureRequirement class: Workflow outputs: minibam: outputSource: sub_run_var_bam/minibam type: File minibamIndex: outputSource: sub_run_var_bam/minibamIndex type: File inputs: inputFileDirectory: type: Directory tumour: type: "TumourType.yaml#TumourType" indel-padding: type: string snv-padding: type: string sv-padding: type: string input-indel: type: File input-snv: type: File input-sv: type: File steps: sub_run_var_bam: run: Variantbam-for-dockstore/variantbam.cwl in: input-bam: source: [inputFileDirectory, tumour] valueFrom: | ${ return { "class":"File", "location": self[0].location + "/" + self[1].bamFileName } } outfile: source: [tumour] valueFrom: $("mini-".concat(self.tumourId).concat(".bam")) snv-padding: snv-padding sv-padding: sv-padding indel-padding: indel-padding input-snv: input-snv input-sv: input-sv input-indel: input-indel out: [minibam, minibamIndex]