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Import fasta_fai in main.nf #85

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merged 4 commits into from
Apr 30, 2024
Merged

Import fasta_fai in main.nf #85

merged 4 commits into from
Apr 30, 2024

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asp8200
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@asp8200 asp8200 commented Mar 15, 2024 •
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Response to comments from Maxime on the upcoming release-PR.

Is the inclusion of (sub)workflows here before the calls to getGenomeAttribute a mistake? (Perhaps it doesn't matter, but in Sarek it is done the over way around.)

I guess we don't want to update the CHANGELOG for this kind of PR, right?

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/bamtofastq 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).

@asp8200 asp8200 mentioned this pull request Mar 15, 2024
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github-actions bot commented Mar 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 32487a8

+| ✅ 168 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-15 21:13:45

@asp8200 asp8200 requested a review from maxulysse March 15, 2024 21:13
@asp8200 asp8200 marked this pull request as ready for review March 15, 2024 21:18
@asp8200 asp8200 mentioned this pull request Mar 18, 2024
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maxulysse
maxulysse reviewed Apr 30, 2024
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LGTM

@asp8200 asp8200 requested a review from maxulysse April 30, 2024 12:16
@asp8200 asp8200 merged commit db5efc6 into nf-core:dev Apr 30, 2024
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@asp8200 asp8200 deleted the import_fasta_fai branch April 30, 2024 14:01
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