tools_cnvkit_batch.cwl

Documentation for cnvkit_batch.cwl

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Introduction

Note: cnvkit batch is a complex command that is capable of running all or part of the cnvkit internal pipeline, depending on the combination of inputs provided to it. In order to take advantage of this, most inputs to this cwl are optional, so that different workflows can use different forms of the command while still using a single cwl file. For further reading, see the relevant cnvkit docs at https://cnvkit.readthedocs.io/en/stable/quickstart.html#build-a-reference-from-normal-samples-and-infer-tumor-copy-ratios https://cnvkit.readthedocs.io/en/stable/pipeline.html#batch In our pipelines, the command form is mainly determined by the components of the reference input. The somatic_exome cwl pipeline provides a fasta file and a normal bam, which causes the batch pipeline to construct a copy number reference (.cnn file) based on the normal bam. The germline_wgs cwl pipeline does not provide a normal bam; instead it passes a cnn reference file as an optional input. This file is intended to be manually generated from a reference normal sample for use in the pipeline. If it is not provided, cnvkit will automatically generate a flat reference file.

Docker Requirement

etal/cnvkit:0.9.5

Inputs

Name	Label	Description	Type	Secondary Files
tumor_bam			File
bait_intervals			File?
reference			[{'type': 'record', 'name': 'cnn_file', 'fields': {'cnn_file': {'type': 'File', 'inputBinding': {'position': 2, 'prefix': '--reference'}, 'doc': 'Previously generated reference.cnn file'}}}, {'type': 'record', 'name': 'fasta_file', 'fields': {'fasta_file': {'type': ['string', 'File'], 'inputBinding': {'position': 2, 'prefix': '--fasta'}}, 'normal_bam': {'type': 'File?', 'inputBinding': {'position': 1}, 'doc': "Normal samples (.bam) used to construct the pooled, paired, or flat reference. If this option is used but no filenames are given, a 'flat' reference will be built. Otherwise, all filenames following this option will be used."}}}]
access		Regions of accessible sequence on chromosomes (.bed), as output by the 'access' command	File?
method		Sequencing protocol used for input data	['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}]
diagram		Create an ideogram of copy ratios on chromosomes as a PDF	boolean?
scatter_plot		Create a whole-genome copy ratio profile as a PDF scatter plot	boolean?
drop_low_coverage		Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples	boolean?
male_reference		Use or assume a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX)	boolean?
target_average_size		Average size of split target bins (results are approximate)	int?

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