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Provide users the ability to not bump stack size. #818

Merged
merged 4 commits into from
Dec 18, 2024
Merged

Provide users the ability to not bump stack size. #818

merged 4 commits into from
Dec 18, 2024

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robsyme
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@robsyme robsyme commented Dec 13, 2024 •
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Not all environments have permissions to set an unlimited stack size. Particularly for smaller samples, this provides the ability to not set an unlimited stack size.

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/ampliseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@robsyme
Provide users the ability to not bump stack size.
7f0c983 
Not all environments have permissions to set an unlimited stack size. Particularly for smaller samples, this provides the ability to not set an unlimited stack size.
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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: 3.0.2.
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 Dec 13, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0c48fde

+| ✅ 297 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-18 07:44:06

@d4straub
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Thanks!

Two points that might be beneficial:

  • since this is related to VSEARCH, I think the best place in nextflow_schema.json would be below vsearch_cluster_id in line 283
  • the CHANGELOG.md could benefit from an update as well.

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robsyme commented Dec 17, 2024

Good suggestions, thanks Daniel. Branch updated with recommendations.

@d4straub
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@nf-core-bot fix linting

d4straub
d4straub approved these changes Dec 18, 2024
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Thanks!

@d4straub d4straub merged commit 55164ab into dev Dec 18, 2024
33 checks passed
@d4straub d4straub deleted the optional-ulimit branch December 18, 2024 09:30
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