#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Per-chromosome pindel" requirements: - class: MultipleInputFeatureRequirement inputs: reference: type: string tumor_cram: type: File secondaryFiles: ["^.crai"] normal_cram: type: File secondaryFiles: ["^.crai"] chromosome: type: string insert_size: type: int default: 400 outputs: per_chromosome_pindel_out: type: File outputSource: cat/pindel_out steps: pindel: run: pindel.cwl in: reference: reference tumor_cram: tumor_cram normal_cram: normal_cram insert_size: insert_size chromosome: chromosome out: [deletions, insertions, tandems, long_insertions, inversions] cat: run: cat_out.cwl in: pindel_outs: [pindel/deletions, pindel/insertions, pindel/tandems, pindel/long_insertions, pindel/inversions] out: [pindel_out]