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hs_metrics.cwl
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hs_metrics.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "HS Metrics workflow"
requirements:
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [^.bai]
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[]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
outputs:
per_base_coverage_metrics:
type: File[]
outputSource: collect_per_base_hs_metrics/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: collect_per_base_hs_metrics/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: collect_per_target_hs_metrics/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: collect_per_target_hs_metrics/hs_metrics
summary_hs_metrics:
type: File[]
outputSource: collect_summary_hs_metrics/hs_metrics
steps:
collect_summary_hs_metrics:
run: ../tools/collect_hs_metrics.cwl
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
bait_intervals:
source: summary_intervals
valueFrom: $(self.file)
target_intervals:
source: summary_intervals
valueFrom: $(self.file)
per_target_coverage:
default: false
per_base_coverage:
default: false
output_prefix:
source: summary_intervals
valueFrom: "summary-$(self.label)"
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
out:
[hs_metrics]
collect_per_base_hs_metrics:
run: ../tools/collect_hs_metrics.cwl
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
bait_intervals:
source: per_base_intervals
valueFrom: $(self.file)
target_intervals:
source: per_base_intervals
valueFrom: $(self.file)
per_target_coverage:
default: false
per_base_coverage:
default: true
output_prefix:
source: per_base_intervals
valueFrom: "base-$(self.label)"
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
out:
[hs_metrics, per_base_coverage_metrics]
collect_per_target_hs_metrics:
run: ../tools/collect_hs_metrics.cwl
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
bait_intervals:
source: per_target_intervals
valueFrom: $(self.file)
target_intervals:
source: per_target_intervals
valueFrom: $(self.file)
per_target_coverage:
default: true
per_base_coverage:
default: false
output_prefix:
source: per_target_intervals
valueFrom: "target-$(self.label)"
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
out:
[hs_metrics, per_target_coverage_metrics]