Bbsplit staging issue #1617
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Bbsplit staging issue #1617
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Dev -> Master for 3.20.0
Dev -> Master for 3.21.0
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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. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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I have made first the changes to modules... |
This updates the bbmap/bbsplit module to address staging issues reported in the original PR. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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Hi @EladH1, thanks for identifying the BBSplit staging issues. I've updated this PR to use the proper solution: updating the bbmap/bbsplit module itself rather than modifying it in the pipeline. The updated module includes the fix from nf-core/modules#9356, which addresses the staging problems while preserving the index reuse functionality. Your commits are preserved in the history and you're credited in the CHANGELOG. |
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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.mdis updated.[- ] Output Documentation in
docs/output.mdis updated.[- ]
CHANGELOG.mdis updated.[ -]
README.mdis updated (including new tool citations and authors/contributors).