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Fix warnings introduced in nextflow 22.10 #504

Merged
merged 5 commits into from
Dec 6, 2022
Merged

Fix warnings introduced in nextflow 22.10 #504

merged 5 commits into from
Dec 6, 2022

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d4straub
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@d4straub d4straub commented Dec 5, 2022 •
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Fix code to avoid warnings such as
WARN: A process with name 'CUTADAPT_SUMMARY_DOUBLEPRIMER' is defined more than once in module script: github-ampliseq/ampliseq/./workflows/../subworkflows/local/cutadapt_workflow.nf -- Make sure to not define the same function as process
that appear from nextflow version 22.10 onward.
Should not have any functional impact whatsoever.

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>).
  • 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 Dec 5, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a6f817d

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-12-05 14:57:55

erikrikarddaniel
erikrikarddaniel approved these changes Dec 5, 2022
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LGTM.

@d4straub
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d4straub commented Dec 6, 2022

Thanks!

@d4straub d4straub merged commit 29d9c3b into nf-core:dev Dec 6, 2022
@d4straub d4straub deleted the fix-warn-introduced-in-nextflow-22.10 branch December 6, 2022 13:38
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@d4straub @erikrikarddaniel