Documentation for pindel.cwl

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Overview

pindel 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
insert_size			int
scatter_count			int
tumor_sample_name			string
normal_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_to_bed	tools/split_interval_list_to_bed.cwl
pindel_cat	subworkflows/pindel_cat.cwl
cat_all	tools/cat_all.cwl
somaticfilter	tools/pindel_somatic_filter.cwl
bgzip	tools/bgzip.cwl
index	tools/index_vcf.cwl
remove_end_tags	tools/remove_end_tags.cwl
reindex	tools/index_vcf.cwl
filter	subworkflows/fp_filter.cwl