#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Add snv and indel bam-readcount files to a vcf" requirements: - class: SubworkflowFeatureRequirement inputs: vcf: type: File secondaryFiles: [.tbi] snv_bam_readcount_tsv: type: File indel_bam_readcount_tsv: type: File data_type: type: - type: enum symbols: ["DNA", "RNA"] sample_name: type: string outputs: annotated_bam_readcount_vcf: type: File outputSource: add_indel_bam_readcount_to_vcf/annotated_bam_readcount_vcf steps: add_snv_bam_readcount_to_vcf: run: ../tools/vcf_readcount_annotator.cwl in: vcf: vcf bam_readcount_tsv: snv_bam_readcount_tsv data_type: data_type sample_name: sample_name variant_type: default: 'snv' out: [annotated_bam_readcount_vcf] add_indel_bam_readcount_to_vcf: run: ../tools/vcf_readcount_annotator.cwl in: vcf: add_snv_bam_readcount_to_vcf/annotated_bam_readcount_vcf bam_readcount_tsv: indel_bam_readcount_tsv data_type: data_type sample_name: sample_name variant_type: default: 'indel' out: [annotated_bam_readcount_vcf]