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Add busco_clean parameter #353

Merged
merged 7 commits into from
Nov 29, 2022
Merged

Add busco_clean parameter #353

merged 7 commits into from
Nov 29, 2022

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prototaxites
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@prototaxites prototaxites commented Nov 15, 2022 •
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Following #341: Added the parameter flag params.busco_clean and corresponding code in workflow/modules/busco.nf, to allow cleaning up of BUSCO work directories following successful execution to reduce file numbers.

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/mag 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>).
  • Usage Documentation in docs/usage.md is updated.
  • 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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github-actions bot commented Nov 15, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 553df5d

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-15 15:49:29

@d4straub
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@nf-core-bot fix linting

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d4straub commented Nov 15, 2022 •
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Thanks for the PR!
Could you add a note to CHANGELOG.md & activate it in a test profile (e.g. by adding busco_clean = true to test.config)?

@prototaxites
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Done! I didn't fork off dev (realising now this was a mistake) so there's some changelog conflicts - hopefully they're not difficult to resolve. This is all rather new to me!

@d4straub
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Yes, nf-core pipelines are developed on the dev branch, not master branch. The file changes are fine now. Lets see how the CI tests run.

skrakau
skrakau reviewed Nov 15, 2022
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Hi, I am just wondering, is there a reason why you do not just delete the whole BUSCO and and augustus_config folders? The relevant BUSCO output files were anyway copied/moved before, or am I missing something here?

@prototaxites
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There's other output in the BUSCO directory, log files in particular, that I thought it was best to leave, in case someone needs to go digging through the work directory to inspect them for some reason (some kind of silent error, maybe).

skrakau
skrakau approved these changes Nov 18, 2022
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Didn't test it, but looks good to me

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I'm going to merge this since nobody else seems to do that ;)

@d4straub d4straub merged commit 6db587e into nf-core:dev Nov 29, 2022
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@prototaxites @d4straub @skrakau @jfy133 @nf-core-bot