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qc_exome_no_verify_bam.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: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [^.bai]
reference:
type: string
bait_intervals:
type: File
target_intervals:
type: File
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
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]