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increase memory for fgbio

Open bounlu opened this issue 1 year ago • 3 comments

fgbio sometimes fails due to OutOfMemoryError for large samples. the default memory is -Xmx1g which may be insufficient. this PR icreases it to -Xmx2g which is more stable and does not hurt the resources much.

PR checklist

  • [x] 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/sarek branch on the nf-core/test-datasets repository.
  • [x] Make sure your code lints (nf-core lint).
  • [x] Ensure the test suite passes (nf-test test tests/ --verbose --profile +docker).
  • [ ] 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).

bounlu avatar Jul 09 '24 05:07 bounlu

This PR is against the master branch :x:

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @bounlu,

It looks like this pull-request is has been made against the nf-core/sarek master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the nf-core/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] avatar Jul 09 '24 05:07 github-actions[bot]

nf-core lint overall result: Failed :x:

Posted for pipeline commit c55d7dd

+| ✅ 192 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   3 tests failed       |-

:x: Test failures:

:heavy_exclamation_mark: Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.2
  • 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!
  • nfcore_yml - nf-core version not set in .nf-core.yml

:grey_question: Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-09 05:29:39

github-actions[bot] avatar Jul 09 '24 05:07 github-actions[bot]

ok, so this should be done first on the modules side, and then propagated upstream back to sarek

maxulysse avatar Jul 11 '24 14:07 maxulysse

This has already been done [upstream in modules])https://github.com/nf-core/modules/blob/master/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf), and then propagated into sarek.

SPPearce avatar Dec 19 '24 15:12 SPPearce