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Enable multiple ploidy values for controlfreec #980

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Enable multiple ploidy values for controlfreec #980

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FriederikeHanssen
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Close #808

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
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github-actions bot commented Mar 28, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 08d314b

+| ✅ 153 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-29 10:50:58

@FriederikeHanssen
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Read the docs: https://github.com/BoevaLab/FREEC/blob/271bef4777119e69ae6eaf1e68051e12fae5e529/scripts/makeGraph2.0.R#L5 I think we don't need to supply the ploidy

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@nf-core-bot fix linting

maxulysse
maxulysse previously approved these changes Mar 30, 2023
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@FriederikeHanssen FriederikeHanssen linked an issue Mar 30, 2023 that may be closed by this pull request
controlfreec with multiple ploidy values results in plotting error #808
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@FriederikeHanssen
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The docs lied to me and need to pass an int into the script afterall..... so reverting to previous changes but will also require a module update so turning this back into draft state for the moment

@FriederikeHanssen FriederikeHanssen marked this pull request as draft March 31, 2023 07:25
@FriederikeHanssen FriederikeHanssen mentioned this pull request Aug 15, 2023
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@FriederikeHanssen
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back to this one: first step: bumping the control freec version, so we can use the new makeGraph script and hopefully solve some issues

@FriederikeHanssen FriederikeHanssen mentioned this pull request Sep 18, 2023
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controlfreec with multiple ploidy values results in plotting error
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