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[GH-236] Fixed regex for hic_map_combinations #237

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Merged
merged 1 commit into from
Jun 24, 2025
Merged

[GH-236] Fixed regex for hic_map_combinations #237

merged 1 commit into from
Jun 24, 2025

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GallVp
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@GallVp GallVp commented Jun 24, 2025

PR checklist

  • hic_map_combinations flag does not take "tag1:tag2" #236
  • 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
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@GallVp GallVp linked an issue Jun 24, 2025 that may be closed by this pull request
hic_map_combinations flag does not take "tag1:tag2" #236
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@GallVp GallVp requested a review from ignacio3437 June 24, 2025 21:17
GallVp
GallVp commented Jun 24, 2025
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tests/hic/hicparam.nf.test
script "./hicparam.nf"
function "checkHiCCombinationsParam"

test(" '' -- fail ") {
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@ignacio3437

Please check if I have left out a common combination.

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The regex doesn't make sense to me but if it passes the tests you described here then I think that covers all the cases I can think of.

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Please try ^\w(\w+)*(\s?\w+(:\w+)?)*$ at https://regex101.com

If you go through the explanations, it will be easier to spot the mistake if any. Thank you!

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github-actions bot commented Jun 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0219626

+| ✅ 180 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗  24 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-24 21:19:04

@GallVp GallVp merged commit 59d72ff into dev Jun 24, 2025
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@GallVp GallVp deleted the fix/gh236 branch June 24, 2025 21:47
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Does this close #236 ?

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GallVp commented Jun 25, 2025

@ignacio3437

Yes, it has fixed the issue on the main branch. We are not closing issues till the code has made into the main branch and a release.

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@ignacio3437 ignacio3437 ignacio3437 approved these changes

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hic_map_combinations flag does not take "tag1:tag2"
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@GallVp @ignacio3437