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Fix bbmap memory #161

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Merged
erikrikarddaniel merged 1 commit into from
Oct 20, 2025
Merged

Fix bbmap memory #161

erikrikarddaniel merged 1 commit into from
Oct 20, 2025

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@erikrikarddaniel erikrikarddaniel commented Oct 20, 2025 •
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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/magmap 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).
  • 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).

Set bbmap process to process_high_memory

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github-actions bot commented Oct 20, 2025

This PR is against the master branch ❌

  • 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 @erikrikarddaniel,

It looks like this pull-request is has been made against the erikrikarddaniel/nf-core-magmap 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 erikrikarddaniel/nf-core-magmap 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!

@erikrikarddaniel erikrikarddaniel changed the base branch from master to dev October 20, 2025 07:27
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github-actions bot commented Oct 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0290d84

+| ✅ 250 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • schema_lint - Input mimetype is missing or empty
  • included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-20 07:28:46

@erikrikarddaniel erikrikarddaniel merged commit 6f5f808 into nf-core:dev Oct 20, 2025
33 of 42 checks passed
@erikrikarddaniel erikrikarddaniel mentioned this pull request Oct 20, 2025
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