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Merged
erikrikarddaniel merged 4 commits into from
Oct 31, 2025
Merged

Improve gff2tsv #168

erikrikarddaniel merged 4 commits into from
Oct 31, 2025

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@erikrikarddaniel erikrikarddaniel commented Oct 29, 2025 •
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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/magmap 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).
  • 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).

Concatenate Prokka tsv files instead of parsing the whole concatenated gff file. For user-provided genomes, first run the parsing code, then pass to concatenation.

This should address #167

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github-actions bot commented Oct 29, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c31f3f4

+| ✅ 240 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/magmap/magmap/subworkflows/local/fastqc_trimgalore/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-29 18:22:33

@erikrikarddaniel erikrikarddaniel merged commit 8839a78 into nf-core:dev Oct 31, 2025
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@erikrikarddaniel erikrikarddaniel deleted the improve-gff2tsv branch October 31, 2025 06:28
@erikrikarddaniel erikrikarddaniel mentioned this pull request Oct 31, 2025
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