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Keep mhaps_freq population indexes when populations come from PMO met… - #120

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PlasmoGenEpi:hotfix/mhaps_freq_index_with_pmo
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Keep mhaps_freq population indexes when populations come from PMO met…#120
kathrynmurie wants to merge 1 commit into
nf-core:devfrom
PlasmoGenEpi:hotfix/mhaps_freq_index_with_pmo

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@kathrynmurie

@kathrynmurie kathrynmurie commented Oct 27, 2026 •
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…adata.

Keep mhaps_freq population indexes when populations come from PMO metadata.

MERGE_TABLES only saw collapsed_amino_acid_calls unless --population_assignment was set, so --pmo_population_fields runs had no SLAF file to merge.

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/plasmodiumdrugres branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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>).
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@kathrynmurie

kathrynmurie commented Oct 27, 2026

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resolves #119

@github-actions

github-actions Bot commented Oct 27, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.1.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Oct 27, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0795f2f

+| ✅ 208 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • 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.

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-plasmodiumdrugres_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-plasmodiumdrugres_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-plasmodiumdrugres_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-27 00:30:49

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@kathrynmurie