/
molecular_qc.cwl
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molecular_qc.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "umi molecular alignment workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
bam:
type: File[]
sample_name:
type: string
read_structure:
type: string[]
reference:
type: string
target_intervals:
type: File
bait_intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
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:
aligned_bam:
type: File
secondaryFiles: [.bai, ^.bai]
outputSource: alignment/aligned_bam
adapter_histogram:
type: File[]
outputSource: alignment/adapter_histogram
duplex_seq_metrics:
type: File[]
outputSource: alignment/duplex_seq_metrics
insert_size_histogram:
type: File
outputSource: qc/insert_size_histogram
insert_size_metrics:
type: File
outputSource: qc/insert_size_metrics
alignment_summary_metrics:
type: File
outputSource: qc/alignment_summary_metrics
hs_metrics:
type: File
outputSource: qc/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: qc/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: qc/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: qc/summary_hs_metrics
flagstats:
type: File
outputSource: qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: qc/verify_bam_id_depth
steps:
alignment:
run: molecular_alignment.cwl
in:
bam: bam
sample_name: sample_name
read_structure: read_structure
reference: reference
target_intervals: target_intervals
out:
[aligned_bam, adapter_histogram, duplex_seq_metrics]
qc:
run: qc_exome.cwl
in:
bam: alignment/aligned_bam
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
out:
[insert_size_metrics, insert_size_histogram, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]