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Deploy nf-validation plugin #63

Merged
merged 1 commit into from
Aug 4, 2023
Merged

Deploy nf-validation plugin #63

merged 1 commit into from
Aug 4, 2023

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SusiJo
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@SusiJo SusiJo commented Aug 2, 2023

This PR includes the nf-validation plugin that was introduced with the nf-core tools version 2.9.
It replace the groovy function extract_csv to parse the samplesheet.

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/bamtofastq 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 Aug 2, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 45f1dd7

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-02 13:27:13

adamrtalbot
adamrtalbot approved these changes Aug 4, 2023
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I gosh darn love nf-validation.

assets/multiqc_config.yml
Comment on lines +2 to +4
This report has been generated by the <a href="https://github.com/nf-core/bamtofastq/tree/dev" target="_blank">nf-core/bamtofastq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/bamtofastq/2.0.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/bamtofastq/dev/docs/output" target="_blank">documentation</a>.
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Is this supposed to be there?

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Yes, this will be passing the linting from the tools version 2.10 onwards :) The old links are not working and are already fixed in the dev version :)

@SusiJo SusiJo merged commit 867b0bb into nf-core:dev Aug 4, 2023
allaway added a commit to allaway/bamtofastq that referenced this pull request Oct 13, 2023
@allaway
tweak usage.md
6ef61ef 
To (partially?) address nf-core#63.
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@SusiJo @adamrtalbot