nf-core / nf-core/createpanelrefs
Add --annotate option for cnvkit
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- Nextflow
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- 11
- Forks
- 16
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Description
Description of feature
I would like to create PON for cnvkit and I noticed that the pipeline currently does not use the cnvkit batch's --annotate option that is used to locate genes in output files. Could you please add it? Without it, when I later create some plots, there are no annotations.
https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=annotate#labeling-target-regions
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the pipeline entry point that invokes cnvkit batch and review how its options are passed. Add support for the requested --annotate option, then verify that generated output contains gene annotations and that the relevant pipeline checks still pass.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100