8000 Fix busco_clean parameter being enabled by default by prototaxites · Pull Request #419 · nf-core/mag · GitHub
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Fix busco_clean parameter being enabled by default #419

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Merged
merged 1 commit into from
Apr 11, 2023
Merged

Fix busco_clean parameter being enabled by default #419

merged 1 commit into from
Apr 11, 2023

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prototaxites
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busco_clean was enabled by default due to an error in the script to check if it is set.

Fixes the check, but also enables it in the binrefinement test because it fails without it due to space limitations. I expect this PR will fail this test due to this.

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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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d3a49b0

+| ✅ 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 2.7.2
  • Run at 2023-03-31 13:49:31

@prototaxites
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Not convinced this worked, but in which case I have no idea what is happening - the number of processes between the two branches are identical...!

d4straub
d4straub approved these changes Apr 11, 2023
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That actually looks like it should work, I approve. If you are still uncertain, let me know and I check (in that case please wait with merging).

@d4straub
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That should allow #395 to pass, right?

9D15

@prototaxites
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That's the theory! I think it will need a little updating to bring it in line with other recent changes.

@prototaxites prototaxites merged commit 0eb5762 into nf-core:dev Apr 11, 2023
@prototaxites prototaxites deleted the busco_clean_fix branch April 11, 2023 13:43
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@d4straub d4straub d4straub approved these changes

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