subworkflows_vcf_eval_cle_gold.cwl

Documentation for vcf_eval_cle_gold.cwl

This page is auto-generated. Do not edit.

Overview

CLE gold vcf evaluation workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
roi_bed			File
query_vcf			File	['.tbi']
normal_cram			File	['^.crai']
tumor_cram			File	['^.crai']
normal_sample_name			string?
tumor_sample_name			string?
gold_vcf			File	['.tbi']
true_negative_bed			File
output_dir			string

Outputs

Name	Label	Description	Type	Secondary Files
output_directory			Directory

Steps

Name	CWL Run
normal_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
tumor_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
gold_vcf_roi	tools/bedtools_intersect.cwl
bgzip_and_index_gold_roi	subworkflows/bgzip_and_index.cwl
query_vcf_pass	tools/select_variants.cwl
query_vcf_pass_roi	tools/bedtools_intersect.cwl
bgzip_and_index_query_pass_roi	subworkflows/bgzip_and_index.cwl
combine_vcf	tools/combine_variants_concordance.cwl
normal_bam_readcount	tools/bam_readcount.cwl
tumor_bam_readcount	tools/bam_readcount.cwl
query_vcf_pass_snv	tools/select_variants.cwl
query_vcf_pass_indel	tools/select_variants.cwl
true_negative_roi	tools/bedtools_intersect.cwl
true_negative_intersect_query_snv	tools/bedtools_intersect.cwl
true_negative_intersect_query_indel	tools/bedtools_intersect.cwl
sompy	tools/sompy.cwl
evaluation	tools/eval_cle_gold.cwl
gather_to_sub_directory	tools/gather_to_sub_directory.cwl