subworkflows_hs_metrics.cwl

Documentation for hs_metrics.cwl

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Overview

HS Metrics workflow

Inputs

Name	Label	Description	Type	Secondary Files
bam			File	['^.bai']
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[]
reference			['string', 'File']	['.fai', '^.dict']
summary_intervals			../types/labelled_file.yml#labelled_file[]

Outputs

Name	Label	Description	Type	Secondary Files
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
summary_hs_metrics			File[]

Steps

Name	CWL Run
collect_summary_hs_metrics	tools/collect_hs_metrics.cwl
collect_per_base_hs_metrics	tools/collect_hs_metrics.cwl
collect_per_target_hs_metrics	tools/collect_hs_metrics.cwl