cwlVersion: v1.0 class: Workflow id: bwa_mem_wf requirements: - class: ScatterFeatureRequirement - class: MultipleInputFeatureRequirement inputs: input_reads: File indexed_reference_fasta: File base_name: string outputs: aligned_bams: type: File[] outputSource: bwa_mem_split/output steps: bwa_input_prepare: run: ../tools/bwa_input_prepare.cwl in: input_bam: input_reads out: [output, rg] expression_updatergsample: run: ../tools/expression_preparerg.cwl in: rg: bwa_input_prepare/rg sample: base_name out: [rg_str] bwa_mem_split: run: ../tools/bwa_mem_split.cwl in: ref: indexed_reference_fasta reads: bwa_input_prepare/output rg: expression_updatergsample/rg_str scatter: [reads] out: [output]