subworkflows_varscan_pre_and_post_processing.cwl

Documentation for varscan_pre_and_post_processing.cwl

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Overview

Varscan 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
strand_filter			int?
min_coverage			int?
min_var_freq			float?
p_value			float?
max_normal_freq			float?
normal_sample_name			string
tumor_sample_name			string
scatter_count			int

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
intervals_to_bed	tools/intervals_to_bed.cwl
varscan	subworkflows/varscan.cwl
merge_scattered_somatic_snvs	tools/picard_merge_vcfs.cwl
merge_scattered_somatic_indels	tools/picard_merge_vcfs.cwl
merge_scattered_somatic_hc_snvs	tools/picard_merge_vcfs.cwl
merge_scattered_somatic_hc_indels	tools/picard_merge_vcfs.cwl
merge_snvs	tools/set_filter_status.cwl
index_merged_snvs	tools/index_vcf.cwl
merge_indels	tools/set_filter_status.cwl
index_merged_indels	tools/index_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	tools/index_vcf.cwl
filter	subworkflows/fp_filter.cwl