#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: 'Unaligned to aligned BAM' requirements: - class: ScatterFeatureRequirement - class: SubworkflowFeatureRequirement - class: MultipleInputFeatureRequirement inputs: bam: type: File reference: type: string readgroup: type: string outputs: tagged_bam: type: File outputSource: align_and_tag/aligned_bam steps: align_and_tag: run: align_and_tag.cwl in: bam: bam readgroup: readgroup reference: reference out: [aligned_bam]