#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "umi per-lane alignment subworkflow" requirements: - class: SubworkflowFeatureRequirement inputs: bam: type: File read_structure: type: string[] reference: string outputs: aligned_bam: type: File secondaryFiles: [^.bai] outputSource: align/aligned_bam adapter_metrics: type: File outputSource: mark_illumina_adapters/metrics steps: extract_umis: run: ../tools/extract_umis.cwl in: bam: bam read_structure: read_structure out: [umi_extracted_bam] mark_illumina_adapters: run: ../tools/mark_illumina_adapters.cwl in: bam: extract_umis/umi_extracted_bam out: [marked_bam, metrics] align: run: ../tools/umi_align.cwl in: bam: mark_illumina_adapters/marked_bam reference: reference out: [aligned_bam]