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update collectrnaseqmetrics memory requirement #474

Merged
merged 6 commits into from
Apr 3, 2024
Merged

update collectrnaseqmetrics memory requirement #474

merged 6 commits into from
Apr 3, 2024

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rannick
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@rannick rannick commented Mar 4, 2024 •
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Update memory requirements

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/rnafusion 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).

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github-actions bot commented Mar 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2448d7f

+| ✅ 167 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-03 10:16:00

@rannick rannick mentioned this pull request Mar 4, 2024
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@rannick rannick requested a review from fevac March 4, 2024 19:01
@rannick rannick self-assigned this Mar 4, 2024
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rannick commented Mar 4, 2024

To be merged once linting works (template 2.13.1 PR merged with dev)

jemten
jemten approved these changes Mar 26, 2024
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Would be good to consider changing to the nf-core version for this module

modules/local/picard/collectrnaseqmetrics/main.nf Outdated
avail_mem = task.memory.giga
}
avail_mem = (task.memory.mega*0.8).intValue()
}
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Small thing but could you align the final }

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rannick commented Apr 3, 2024

Replacement by the nf-core module is planned.

@rannick rannick merged commit 4fe1a5d into dev Apr 3, 2024
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@rannick rannick deleted the fix_rnaseqmetrics_mem branch April 3, 2024 10:40
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@jemten jemten jemten approved these changes

@apeltzer apeltzer apeltzer approved these changes

@fevac fevac Awaiting requested review from fevac

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