subworkflows_cnvkit_single_sample.cwl

Documentation for cnvkit_single_sample.cwl

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Overview

Subworkflow that runs cnvkit in single sample mode and returns a vcf file

Inputs

Name	Label	Description	Type	Secondary Files
fasta_reference			['string', 'File']	['.fai']
tumor_bam			File
method			['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}]
diagram			boolean?
scatter_plot			boolean?
drop_low_coverage			boolean?
male_reference			boolean?
reference_cnn			File?
cnvkit_vcf_name			string
segment_filter			['null', {'type': 'enum', 'symbols': ['ampdel', 'ci', 'cn', 'sem']}]

Outputs

Name	Label	Description	Type	Secondary Files
cn_diagram			File?
cn_scatter_plot			File?
tumor_antitarget_coverage			File
tumor_target_coverage			File
tumor_bin_level_ratios			File
tumor_segmented_ratios			File
cnvkit_vcf			File

Steps

Name	CWL Run
cnvkit_main	tools/cnvkit_batch.cwl
cns_to_vcf	tools/cnvkit_vcf_export.cwl