subworkflows_qc_wgs.cwl

Documentation for qc_wgs.cwl

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Overview

WGS QC workflow

Inputs

Name	Label	Description	Type	Secondary Files
sample_name			string?
bam			File	['^.bai']
reference			['string', 'File']	['.fai', '^.dict']
intervals			File
omni_vcf			File	['.tbi']
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
gc_bias_metrics			File
gc_bias_metrics_chart			File
gc_bias_metrics_summary			File
wgs_metrics			File
flagstats			File
verify_bam_id_metrics			File
verify_bam_id_depth			File
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
summary_hs_metrics			File[]
bamcoverage_bigwig			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_gc_bias_metrics	tools/collect_gc_bias_metrics.cwl
collect_wgs_metrics	tools/collect_wgs_metrics.cwl
samtools_flagstat	tools/samtools_flagstat.cwl
verify_bam_id	tools/verify_bam_id.cwl
collect_hs_metrics	subworkflows/hs_metrics.cwl
cgpbigwig_bamcoverage	tools/bam_to_bigwig.cwl