#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "bam to trimmed fastqs" requirements: - class: MultipleInputFeatureRequirement - class: SubworkflowFeatureRequirement - class: InlineJavascriptRequirement inputs: bam: type: File adapters: type: File adapter_trim_end: type: string adapter_min_overlap: type: int max_uncalled: type: int min_readlength: type: int outputs: fastqs: type: File[] outputSource: trim_fastq/fastqs fastq1: type: File outputSource: trim_fastq/fastq1 fastq2: type: File outputSource: trim_fastq/fastq2 steps: bam_to_fastq: run: ../tools/bam_to_fastq.cwl in: bam: bam out: [fastq1, fastq2] trim_fastq: run: ../tools/trim_fastq.cwl in: reads1: bam_to_fastq/fastq1 reads2: bam_to_fastq/fastq2 adapters: adapters adapter_trim_end: adapter_trim_end adapter_min_overlap: adapter_min_overlap max_uncalled: max_uncalled min_readlength: min_readlength out: [fastqs, fastq1, fastq2]