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Fix crisprcleanr input file #192

Merged
merged 4 commits into from
Aug 21, 2024
Merged

Fix crisprcleanr input file #192

merged 4 commits into from
Aug 21, 2024

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LaurenceKuhl
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In the process CRISPRCLEANR_NORMALIZE I use a custom library file which results in running the code in the else loop. The column name of the count_file is "Gene" and not "gene" resulting in an error. @bolenala mentions it here : #161 and provides a fix :)

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github-actions bot commented Aug 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 671ca2f

+| ✅ 224 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-21 07:23:49

mirpedrol
mirpedrol approved these changes Aug 20, 2024
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LGTM!

The change to the module should also be applied to the nf-core/modules repo. If you fancy contributing, you could add your fix there @bolenala 😄

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@LaurenceKuhl LaurenceKuhl merged commit bdb7682 into nf-core:dev Aug 21, 2024
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@LaurenceKuhl LaurenceKuhl mentioned this pull request Sep 17, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

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@LaurenceKuhl @mirpedrol