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Add pipeline-level nf-test #95

Merged
merged 22 commits into from
Nov 17, 2024
Merged

Add pipeline-level nf-test #95

merged 22 commits into from
Nov 17, 2024

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atrigila
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@atrigila atrigila commented Nov 14, 2024 •
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Closes #93

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • CHANGELOG.md is updated.

@atrigila atrigila self-assigned this Nov 14, 2024
@nschcolnicov nschcolnicov mentioned this pull request Nov 14, 2024
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 2.14.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Nov 14, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 25e4fcf

+| ✅ 199 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-15 19:56:21

@atrigila
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A suffix that is added in write_out_prepared_gex.R is unstable. Even with the same input files, sometimes it appends that to the files and others it does not, creating a conflict with snapshots. I am going to modify that line to see if this solves the filename issue.

@atrigila
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The tests work well locally but produce files with different names in the CI and therefore fail.

@atrigila
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The issue is with multiqc outputs and versions in the CI. These differ from the local, most up-to-date multiqc. We switch back to an old multiqc version and re-test.

@atrigila
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Shoutout to @nschcolnicov for finding a solution to this issue🥇

@atrigila atrigila marked this pull request as ready for review November 15, 2024 20:17
@apeltzer apeltzer merged commit 35854c5 into nf-core:dev Nov 17, 2024
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@apeltzer apeltzer apeltzer approved these changes

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@atrigila @nf-core-bot @apeltzer @nschcolnicov