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Bbsplit staging issue #1617

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Bbsplit staging issue #1617

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@EladH1
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@EladH1 EladH1 commented Nov 5, 2025

PR checklist

  • [+] This comment contains a description of changes (with reason).
    Description: Fixed BBSplit staging issues by adding stageInMode 'copy' and removing complex timestamp fixing logic that was causing problems with staged index files.
    Reason: The previous script had staging issues that prevented proper index file handling.
    The code of bbsplit modified in place the .summary.txt --> sometimes even deleting the last modified line.
    This change also improves the resume of bbsplit as the .summary.txt file stay the same.

  • [+ ] If you've fixed a bug or added code that should be tested, add tests!
    I fixed a bug in the BBSplit module. This is now run better

  • [- ] 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 pipelines lint).
    linting has issue here but not with my code

  • [+ ] 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).

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nf-core-bot commented Nov 5, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Nov 5, 2025

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 75b7c47

+| ✅ 288 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-11-05 11:28:11

@EladH1 EladH1 enabled auto-merge November 5, 2025 12:31
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@EladH1 @nf-core-bot @maxulysse @pinin4fjords