Documentation for phase_vcf.cwl

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Overview

phase VCF

Inputs

Name	Label	Description	Type	Secondary Files
somatic_vcf			File	['.tbi']
germline_vcf			File
reference			['string', 'File']	['.fai', '^.dict']
reference_dict			File
bam			File	${if (self.nameext === ".bam") {return self.basename + ".bai"} else {return self.basename + ".crai"}}
normal_sample_name			string
tumor_sample_name			string

Outputs

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

Steps

Name	CWL Run
rename_germline_vcf	tools/replace_vcf_sample_name.cwl
index_renamed_germline	tools/index_vcf.cwl
select_somatic_tumor_sample	tools/select_variants.cwl
index_filtered_somatic	tools/index_vcf.cwl
combine_variants	tools/pvacseq_combine_variants.cwl
sort	tools/sort_vcf.cwl
bgzip_and_index	subworkflows/bgzip_and_index.cwl
phase_vcf	tools/read_backed_phasing.cwl
bgzip_and_index_phased_vcf	subworkflows/bgzip_and_index.cwl