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#!/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]
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