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Fix groovyjarjarantlr4.v4.runtime.LexerNoViableAltException #721

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merged 3 commits into from Mar 26, 2024
Merged

Fix groovyjarjarantlr4.v4.runtime.LexerNoViableAltException #721

merged 3 commits into from Mar 26, 2024

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d4straub
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@d4straub d4straub commented Mar 26, 2024 •
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Whenever version 2.8.0 of the pipeline started, the message unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException appeared, causing confusion. The cause was a missing \ in a nf-core module, thats now fixed.

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/ampliseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
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@d4straub d4straub added this to the 2.9.0 milestone Mar 26, 2024
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github-actions bot commented Mar 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7a27dc4

+| ✅ 191 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-26 13:07:41

erikrikarddaniel
erikrikarddaniel approved these changes Mar 26, 2024
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So, you didn't update upstream?

@d4straub d4straub mentioned this pull request Mar 26, 2024
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Well, I troubleshooted for a while in the pipeline and fixed it first here. But yes, that should be fixed upstream, made an issue in nf-core/modules for now.

@d4straub d4straub merged commit a9a6d82 into nf-core:dev Mar 26, 2024
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@d4straub d4straub deleted the fix-groovyjarjarantlr4.v4.runtime.LexerNoViableAltException branch March 26, 2024 14:24
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