subworkflows_mutect.cwl

Documentation for mutect.cwl

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Overview

mutect parallel workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
tumor_bam			File	['^.bai', '.bai']
normal_bam			File?	['^.bai']
interval_list			File
scatter_count			int
tumor_sample_name			string

Outputs

Name	Label	Description	Type	Secondary Files
unfiltered_vcf			File	['.tbi']
filtered_vcf			File	['.tbi']

Steps

Name	CWL Run
split_interval_list	tools/split_interval_list.cwl
mutect	tools/mutect.cwl
merge	tools/merge_vcf.cwl
index	tools/index_vcf.cwl
filter	subworkflows/fp_filter.cwl