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Put functions within closure to evaluate them properly. #166

Merged
merged 1 commit into from
Feb 8, 2024
Merged

Put functions within closure to evaluate them properly. #166

merged 1 commit into from
Feb 8, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Feb 8, 2024 •
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Puts functions in config file within closure so that they are evaluated properly.

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).

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github-actions bot commented Feb 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 28e73b1

+| ✅ 186 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 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 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 2.12.1
  • Run at 2024-02-08 12:09:01

@subwaystation
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Thanks @adamrtalbot :)

@subwaystation subwaystation merged commit 1d2915b into dev Feb 8, 2024
15 checks passed
@adamrtalbot adamrtalbot deleted the config_function_fix branch February 9, 2024 11:46
@adamrtalbot
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See nextflow-io/nextflow#4722 for related issue - there may be some more nuance to this then we anticipated. Still, this fix is good enough for now.

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@subwaystation subwaystation Awaiting requested review from subwaystation

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