subworkflows_varscan.cwl

Documentation for varscan.cwl

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Overview

varscan somatic workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
tumor_bam			File	['^.bai']
normal_bam			File	['^.bai']
roi_bed			File?
strand_filter			int?
min_coverage			int?
min_var_freq			float?
p_value			float?
max_normal_freq			float?

Outputs

Name	Label	Description	Type	Secondary Files
snvs			File
indels			File
somatic_hc_snvs			File
somatic_snvs			File
germline_hc_snvs			File
germline_snvs			File
loh_hc_snvs			File
loh_snvs			File
somatic_hc_indels			File
somatic_indels			File
germline_hc_indels			File
germline_indels			File
loh_hc_indels			File
loh_indels			File

Steps

Name	CWL Run
somatic	tools/varscan_somatic.cwl
process_somatic_snvs	tools/varscan_process_somatic.cwl
process_somatic_indels	tools/varscan_process_somatic.cwl