subworkflows_cram_to_cnvkit.cwl

Documentation for cram_to_cnvkit.cwl

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Overview

Subworkflow to allow calling cnvkit with cram instead of bam files

Inputs

Name	Label	Description	Type	Secondary Files
normal_cram			File	['^.crai']
tumor_cram			File	['^.crai']
reference			string
bait_intervals			File
access			File?
method			string?
diagram			boolean?
scatter_plot			boolean?
drop_low_coverage			boolean?

Outputs

Name	Label	Description	Type	Secondary Files
intervals_antitarget			File?
intervals_target			File?
normal_antitarget_coverage			File
normal_target_coverage			File
reference_coverage			File?
cn_diagram			File?
cn_scatter_plot			File?
tumor_antitarget_coverage			File
tumor_target_coverage			File
tumor_bin_level_ratios			File
tumor_segmented_ratios			File

Steps

Name	CWL Run
normal_cram_to_bam	tools/cram_to_bam.cwl
tumor_cram_to_bam	tools/cram_to_bam.cwl
run_cnvkit	tools/cnvkit_batch.cwl