Documentation for strelka_and_post_processing.cwl

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Overview

strelka workflow

Inputs

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

Outputs

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

Steps

Name	CWL Run
strelka	tools/strelka.cwl
process	subworkflows/strelka_process_vcf.cwl
merge	tools/merge_vcf.cwl
rename_tumor_sample	tools/replace_vcf_sample_name.cwl
rename_normal_sample	tools/replace_vcf_sample_name.cwl
index_full	tools/index_vcf.cwl
region_filter	tools/select_variants.cwl
filter	subworkflows/fp_filter.cwl