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Resolve merge conflicts #238

Merged
merged 6 commits into from
Jan 30, 2025
Merged

Resolve merge conflicts #238

merged 6 commits into from
Jan 30, 2025

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heuermh
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@heuermh heuermh commented Jan 30, 2025

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/pangenome branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@heuermh heuermh requested a review from subwaystation January 30, 2025 16:42
@heuermh heuermh mentioned this pull request Jan 30, 2025
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github-actions bot commented Jan 30, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 63b639b

+| ✅ 232 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 1.1.3
  • 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!
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - pggb.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - odgi_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - community.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-01-30 16:43:31

@heuermh
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heuermh commented Jan 30, 2025

Thank you, @LeonHafner!

@heuermh heuermh merged commit d292756 into nf-core:dev Jan 30, 2025
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@LeonHafner LeonHafner LeonHafner approved these changes

@subwaystation subwaystation Awaiting requested review from subwaystation

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@heuermh @LeonHafner @subwaystation @maxulysse