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Add optional targets argument to CNVkit #13

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merged 5 commits into from
Jan 15, 2024
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lescai
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@lescai lescai commented Jan 14, 2024

PR checklist

  • Reasons:
    The current version of this tool defaults to the WGS method and has no option to pass the necessary target intervals for either hybrid method (which would be default of CNVkit) or amplicon method.
    This PR simply adds a cnvkit_targets parameter, which can be used if the user wishes to default to the hybrid method. The channel defaults to the usual empty tuple, should the targets bed file not be provided, leaving the current execution as is.
  • If you've fixed a bug or added code that should be tested, add tests!
    The modified pipeline has been successfully tested on real-life data, with either hybrid or current WGS method.
  • No new data were needed for this change
  • Make sure your code lints (nf-core lint): current version of dev - please note that some lint failures occur due to mismatch in template
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md has been updated to explain the necessary modification of config file as well as the new optional parameter usage.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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Lgtm

@lescai lescai merged commit add0a30 into nf-core:dev Jan 15, 2024
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2 participants