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make the use of chunks explicit #160

Merged
merged 2 commits into from
Oct 31, 2023
Merged

make the use of chunks explicit #160

merged 2 commits into from
Oct 31, 2023

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subwaystation
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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/pangenome 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).

This sets the default wfmash_chunks to null instead of 1 so that it is clear that we don't do chunks when the parameter is not set at all.

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github-actions bot commented Oct 31, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit baf2d76

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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 WorkflowPangenome.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-31 08:56:42

@subwaystation subwaystation merged commit db11552 into dev Oct 31, 2023
17 checks passed
@heuermh heuermh deleted the wfmash_power_up branch February 22, 2024 16:13
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