#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Per-region pindel" requirements: - class: MultipleInputFeatureRequirement inputs: reference: type: - string - File secondaryFiles: [.fai, ^.dict] tumor_bam: type: File secondaryFiles: ["^.bai"] normal_bam: type: File secondaryFiles: ["^.bai"] region_file: type: File insert_size: type: int default: 400 tumor_sample_name: type: string normal_sample_name: type: string outputs: per_region_pindel_out: type: File outputSource: cat/pindel_out steps: pindel: run: ../tools/pindel.cwl in: reference: reference tumor_bam: tumor_bam normal_bam: normal_bam insert_size: insert_size region_file: region_file tumor_sample_name: tumor_sample_name normal_sample_name: normal_sample_name out: [deletions, insertions, tandems, long_insertions, inversions] cat: run: ../tools/cat_out.cwl in: pindel_outs: [pindel/deletions, pindel/insertions, pindel/tandems, pindel/long_insertions, pindel/inversions] out: [pindel_out]