/
qc_exome.cwl
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/
qc_exome.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Exome QC workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [^.bai]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
bait_intervals:
type: File
target_intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
default: ALL_READS
minimum_mapping_quality:
type: int?
minimum_base_quality:
type: int?
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
outputs:
insert_size_metrics:
type: File
outputSource: collect_insert_size_metrics/insert_size_metrics
insert_size_histogram:
type: File
outputSource: collect_insert_size_metrics/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: collect_alignment_summary_metrics/alignment_summary_metrics
hs_metrics:
type: File
outputSource: collect_roi_hs_metrics/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/summary_hs_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: ../tools/collect_insert_size_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level: picard_metric_accumulation_level
out:
[insert_size_metrics, insert_size_histogram]
collect_alignment_summary_metrics:
run: ../tools/collect_alignment_summary_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level: picard_metric_accumulation_level
out:
[alignment_summary_metrics]
collect_roi_hs_metrics:
run: ../tools/collect_hs_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
bait_intervals: bait_intervals
target_intervals: target_intervals
per_target_coverage:
default: false
per_base_coverage:
default: false
output_prefix:
valueFrom: "roi"
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
out:
[hs_metrics]
collect_detailed_hs_metrics:
run: hs_metrics.cwl
in:
bam: bam
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
reference: reference
summary_intervals: summary_intervals
out:
[per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]
samtools_flagstat:
run: ../tools/samtools_flagstat.cwl
in:
bam: bam
out: [flagstats]
select_variants:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: omni_vcf
interval_list: target_intervals
out:
[filtered_vcf]
verify_bam_id:
run: ../tools/verify_bam_id.cwl
in:
bam: bam
vcf: select_variants/filtered_vcf
out:
[verify_bam_id_metrics, verify_bam_id_depth]