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

Fetched 2023-01-04 19:36:19 GMT
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Inputs

ID Type Title Doc
method
diagram Boolean (Optional)
tumor_bam File
scatter_plot Boolean (Optional)
reference_cnn File (Optional)
male_reference Boolean (Optional)
segment_filter
cnvkit_vcf_name String
fasta_reference File
drop_low_coverage Boolean (Optional)

Steps

ID Runs Label Doc
cns_to_vcf
../tools/cnvkit_vcf_export.cwl (CommandLineTool)
Convert default cnvkit .cns output to standard vcf format
cnvkit_main
../tools/cnvkit_batch.cwl (CommandLineTool)

Outputs

ID Type Label Doc
cn_diagram File (Optional)
cnvkit_vcf File
cn_scatter_plot File (Optional)
tumor_target_coverage File
tumor_bin_level_ratios File
tumor_segmented_ratios File
tumor_antitarget_coverage File
Permalink: https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/subworkflows/cnvkit_single_sample.cwl