Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

rannick
Copy link
Collaborator

@rannick rannick commented Mar 4, 2024 •
edited

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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 4, 2024 •
edited

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
Closed
10 tasks
@rannick rannick requested a review from fevac March 4, 2024 19:01
@rannick rannick self-assigned this Mar 4, 2024
@rannick
Copy link
Collaborator Author

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
View reviewed changes
Copy link
Contributor

@jemten jemten left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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()
}
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Small thing but could you align the final }

@rannick
Copy link
Collaborator Author

rannick commented Apr 3, 2024

Replacement by the nf-core module is planned.

@rannick rannick merged commit 4fe1a5d into dev Apr 3, 2024
6 checks passed
@rannick rannick deleted the fix_rnaseqmetrics_mem branch April 3, 2024 10:40
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@apeltzer apeltzer apeltzer approved these changes

@jemten jemten jemten approved these changes

@fevac fevac Awaiting requested review from fevac

Assignees

@rannick rannick

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
3 participants
@rannick @apeltzer @jemten