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Reuse bbsplit index and don't keep overwriting #1226

Merged
merged 7 commits into from
Feb 28, 2024
Merged

Reuse bbsplit index and don't keep overwriting #1226

merged 7 commits into from
Feb 28, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 28, 2024 •
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Pulling in important BBSplit fix - see nf-core/modules#5005 for more info.

Also fixing a broken config selector for BBSplit

PR checklist

Closes #1225

  • 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/rnaseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@pinin4fjords pinin4fjords mentioned this pull request Feb 28, 2024
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github-actions bot commented Feb 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 699634b

+| ✅ 170 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-28 16:30:21

@pinin4fjords pinin4fjords linked an issue Feb 28, 2024 that may be closed by this pull request
BBSPLIT implementation broken #1225
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@pinin4fjords pinin4fjords merged commit ed91711 into dev Feb 28, 2024
27 checks passed
@pinin4fjords pinin4fjords deleted the bbsplit_no_overwrite branch February 28, 2024 17:09
@pinin4fjords pinin4fjords mentioned this pull request Mar 12, 2024
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@maxulysse maxulysse maxulysse approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

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BBSPLIT implementation broken
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@pinin4fjords @maxulysse