subworkflows_qc_exome_no_verify_bam.cwl

Documentation for qc_exome_no_verify_bam.cwl

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Overview

Exome QC workflow

Inputs

Name	Label	Description	Type	Secondary Files
bam			File	['^.bai']
reference			['string', 'File']	['.fai', '^.dict']
bait_intervals			File
target_intervals			File
picard_metric_accumulation_level			string
minimum_mapping_quality			int?
minimum_base_quality			int?
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
summary_intervals			../types/labelled_file.yml#labelled_file[]

Outputs

Name	Label	Description	Type	Secondary Files
insert_size_metrics			File
insert_size_histogram			File
alignment_summary_metrics			File
hs_metrics			File
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
summary_hs_metrics			File[]
flagstats			File

Steps

Name	CWL Run
collect_insert_size_metrics	tools/collect_insert_size_metrics.cwl
collect_alignment_summary_metrics	tools/collect_alignment_summary_metrics.cwl
collect_roi_hs_metrics	tools/collect_hs_metrics.cwl
collect_detailed_hs_metrics	subworkflows/hs_metrics.cwl
samtools_flagstat	tools/samtools_flagstat.cwl