#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "WGS QC workflow" requirements: - class: SubworkflowFeatureRequirement inputs: bam: type: File secondaryFiles: [^.bai] reference: type: File secondaryFiles: [.fai] intervals: type: File omni_vcf: type: File secondaryFiles: [.tbi] outputs: insert_size_metrics: type: File outputSource: collect_insert_size_metrics/insert_size_metrics alignment_summary_metrics: type: File outputSource: collect_alignment_summary_metrics/alignment_summary_metrics gc_bias_metrics: type: File outputSource: collect_gc_bias_metrics/gc_bias_metrics gc_bias_metrics_chart: type: File outputSource: collect_gc_bias_metrics/gc_bias_metrics_chart gc_bias_metrics_summary: type: File outputSource: collect_gc_bias_metrics/gc_bias_metrics_summary wgs_metrics: type: File outputSource: collect_wgs_metrics/wgs_metrics flagstats: type: File outputSource: samtools_flagstat/flagstats verify_bam_id_metrics: type: File outputSource: verify_bam_id/verify_bam_id_metrics verify_bam_id_depth: type: File outputSource: verify_bam_id/verify_bam_id_depth steps: collect_insert_size_metrics: run: collect_insert_size_metrics.cwl in: bam: bam out: [insert_size_metrics] collect_alignment_summary_metrics: run: collect_alignment_summary_metrics.cwl in: bam: bam reference: reference out: [alignment_summary_metrics] collect_gc_bias_metrics: run: collect_gc_bias_metrics.cwl in: bam: bam reference: reference out: [gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary] collect_wgs_metrics: run: collect_wgs_metrics.cwl in: bam: bam reference: reference intervals: intervals out: [wgs_metrics] samtools_flagstat: run: samtools_flagstat.cwl in: bam: bam out: [flagstats] verify_bam_id: run: verify_bam_id.cwl in: bam: bam vcf: omni_vcf out: [verify_bam_id_metrics, verify_bam_id_depth]