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47 lines
1.4 KiB
YAML
47 lines
1.4 KiB
YAML
name: cnvkit_reference
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description:
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keywords:
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- cnvkit
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- reference
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tools:
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- cnvkit:
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description: |
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CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data.
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It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
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homepage: https://cnvkit.readthedocs.io/en/stable/index.html
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documentation: https://cnvkit.readthedocs.io/en/stable/index.html
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tool_dev_url: https://github.com/etal/cnvkit
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doi: 10.1371/journal.pcbi.1004873
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licence: ["Apache-2.0"]
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input:
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- fasta:
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type: file
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description: File containing reference genome
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pattern: "*.{fasta}"
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- targets:
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type: file
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description: File containing genomic regions
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pattern: "*.{bed}"
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- antitargets:
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type: file
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description: File containing off-target genomic regions
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pattern: "*.{bed}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reference:
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type: file
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description: File containing a copy-number reference (required for CNV calling in tumor_only mode)
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pattern: "*.{cnn}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@SusiJo"
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