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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Exome QC workflow"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [^.bai]
reference:
type: File
secondaryFiles: [.fai]
bait_intervals:
type: File
target_intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
collect_hs_metrics_per_target_coverage:
type: boolean?
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
hs_metrics:
type: File
outputSource: collect_hs_metrics/hs_metrics
per_target_coverage_metrics:
type: File?
outputSource: collect_hs_metrics/per_target_coverage_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_hs_metrics:
run: collect_hs_metrics.cwl
in:
bam: bam
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
per_target_coverage: collect_hs_metrics_per_target_coverage
out:
[hs_metrics, per_target_coverage_metrics]
samtools_flagstat:
run: samtools_flagstat.cwl
in:
bam: bam
out: [flagstats]
select_variants:
run: ../detect_variants/select_variants.cwl
in:
reference: reference
vcf: omni_vcf
interval_list: target_intervals
out:
[filtered_vcf]
verify_bam_id:
run: verify_bam_id.cwl
in:
bam: bam
vcf: select_variants/filtered_vcf
out:
[verify_bam_id_metrics, verify_bam_id_depth]
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