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Add nf-test for local module blat_mirna #387

Merged
merged 6 commits into from
Aug 27, 2024
Merged

Add nf-test for local module blat_mirna #387

merged 6 commits into from
Aug 27, 2024

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atrigila
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@atrigila atrigila commented Aug 26, 2024 •
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This PR:

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • CHANGELOG.md is updated.

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github-actions bot commented Aug 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f525be2

+| ✅ 213 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 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!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-27 11:42:54

@atrigila atrigila marked this pull request as ready for review August 26, 2024 14:55
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This PR focuses on solving #354. Migration to a nf-core module will be solved in issue #368

@atrigila atrigila mentioned this pull request Aug 26, 2024
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nschcolnicov
nschcolnicov reviewed Aug 26, 2024
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conf/test_contamination.config
@@ -0,0 +1,41 @@
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This test profile is almost identical to test_full_filter_contamination isn't it?

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Yes! The input samplesheet is smaller, though

apeltzer
apeltzer approved these changes Aug 26, 2024
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Looks reasonable to me - the close relationship to the existing tests is ok as this tackles solely the blat_mirna case I think.

@apeltzer apeltzer merged commit 0e95690 into nf-core:dev Aug 27, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@apeltzer apeltzer apeltzer approved these changes

@grst grst Awaiting requested review from grst

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@atrigila @apeltzer @nschcolnicov