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Merging template updates 2.12 #697

Merged
merged 8 commits into from
Feb 1, 2024
Merged

Merging template updates 2.12 #697

merged 8 commits into from
Feb 1, 2024

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d4straub
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@d4straub d4straub commented Feb 1, 2024 •
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Template update 2.12

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.
  • 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 Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 93a5869

+| ✅ 191 tests passed       |+
#| ❔   6 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 2.12.1
  • Run at 2024-02-01 13:21:37

erikrikarddaniel
erikrikarddaniel approved these changes Feb 1, 2024
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You're quick! :-)

@d4straub
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d4straub commented Feb 1, 2024

Thanks, but somehow I cannot get nf-core tools/linting locally to work and I need to correct those failing tests ;)

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d4straub commented Feb 1, 2024

Only remaining issue is

 ╭─ [✗] 1 Subworkflow Test Failed ──────────────────────────────────────────────╮
│                           ╷                        ╷                         │
│ Subworkflow name          │ File path              │ Test message            │
│╶──────────────────────────┼────────────────────────┼────────────────────────╴│
│ fasta_newick_epang_gappa  │ subworkflows/nf-core/… │ Local copy of           │
│                           │                        │ subworkflow does not    │
│                           │                        │ match remote            │
│                           ╵                        ╵                         │
╰──────────────────────────────────────────────────────────────────────────────╯

I am a little surprised that this is an issue, will see what I can do about it.

@d4straub
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d4straub commented Feb 1, 2024

For posterity: updating subworkflow fasta_newick_epang_gappa was tricky because module mafft was changed and the most recent version isnt compatible with the subworkflow:

Process NFCORE_AMPLISEQ:AMPLISEQ:FASTA_NEWICK_EPANG_GAPPA:MAFFT declares 6 input channels but 2 were specified

Therefore I fixed the mafft module at version feb29be775d9e41750180539e9a3bdce801d0609 in .nf-core.yml. That must be removed again in case the module should be updated to another version.

@d4straub d4straub merged commit bc1a10e into nf-core:dev Feb 1, 2024
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@d4straub d4straub deleted the merging-template-updates-2.12 branch February 1, 2024 13:57
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@d4straub @erikrikarddaniel @nf-core-bot