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fix wfmash_sparse_map parameter #152

Merged
merged 9 commits into from
Sep 21, 2023
Merged

fix wfmash_sparse_map parameter #152

merged 9 commits into from
Sep 21, 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).

Previously, one could only select numbers as input and not "auto". This is a fix.

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github-actions bot commented Sep 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 90ebc5d

+| ✅ 154 tests passed       |+
#| ❔   1 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ 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 2.9
  • Run at 2023-09-21 19:08:52

maxulysse
maxulysse approved these changes Sep 21, 2023
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LGTM.

What you could do to make sure all is right for this params, is do some inside params validation and exit early if you have something that is neither auto nor a number between 0 and 1

@subwaystation subwaystation merged commit 0d66ee3 into dev Sep 21, 2023
16 checks passed
@heuermh heuermh deleted the wfmash_sparse_map branch February 22, 2024 16:13
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@maxulysse maxulysse maxulysse approved these changes

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@subwaystation @maxulysse