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Add xengsort contamination removal support#2161

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xengsort
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Add xengsort contamination removal support#2161
famosab wants to merge 10 commits intodevfrom
xengsort

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@famosab famosab commented Mar 25, 2026 •
edited by xinghansun
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Description

Add xengsort as an additional contamination removal option in nf-core/sarek (follow-up to #1578 and the nf-core Hackathon project sarek-remove-genome-contaminants proposed by @apsteinberg).

What changed

  • Add new modules: xengsort index and xengsort classify.
  • Wire xengsort index through prepare_genome and classify through fastq_preprocess_gatk.
  • Add new params and schema entries:
    • xengsort_host_fasta
    • xengsort_index
    • xengsort_nobjects
    • xengsort_kmersize
    • save_xengsort_reads
  • Add xengsort tests and update snapshots.
  • Update docs (README.md, docs/output.md, docs/usage.md).
  • Sync ro-crate-metadata.json with updated docs.

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/sarek 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>).
  • 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).

Validation runs

  • nf-test test tests/xengsort.nf.test --profile test, docker
  • nf-test test modules/local/xengsort/index/tests/main.nf.test --profile docker
  • nf-test test modules/local/xengsort/classify/tests/main.nf.test --profile docker
  • nf-test test subworkflows/local/prepare_genome/tests/xengsort.nf.test --profile test, docker
  • nf-core pipelines lint

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nf-core-bot commented Mar 25, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Mar 25, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 715bc38

+| ✅ 224 tests passed       |+
#| ❔  13 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-27 15:17:17

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Reviewers

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

At least 1 approving review is required to merge this pull request.

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@xinghansun xinghansun

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@famosab @nf-core-bot @xinghansun