subworkflows_pindel_region.cwl

Documentation for pindel_region.cwl

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Overview

Run pindel on provided region

Inputs

Name	Label	Description	Type	Secondary Files
reference			string
tumor_bam			File	['^.bai']
normal_bam			File	['^.bai']
region_file			File
insert_size			int
ref_name			string?
output_name			string?
tumor_sample_name			string
normal_sample_name			string

Outputs

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

Steps

Name	CWL Run
pindel_region	tools/pindel.cwl
cat	tools/cat_out.cwl
pindel2vcf	tools/pindel2vcf.cwl
fix_vcf_header	tools/fix_vcf_header.cwl
remove_end_tags	tools/remove_end_tags.cwl
index	tools/index_vcf.cwl