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Add metagroot domain annot#89

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add-metagroot-domain-annot
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Add metagroot domain annot#89
angelphanth wants to merge 2 commits into
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add-metagroot-domain-annot

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@angelphanth angelphanth commented Mar 13, 2026

PR checklist

This pull request adds support for domain annotation using the MetagRoot database in the protein annotator pipeline. It introduces new parameters for controlling the use of MetagRoot, integrates a new wget module for downloading the database, and updates relevant subworkflows, configuration files, and documentation to reflect these changes.

MetagRoot domain annotation integration:

  • Added parameters (skip_mroot, mroot_db, mroot_latest_link) to control the inclusion and sourcing of the MetagRoot HMM database in nextflow.config, nextflow_schema.json, and related config/test files. [1] [2] [3]
  • Updated the DOMAIN_ANNOTATION subworkflow to download, extract, and use the MetagRoot HMM database for domain annotation if not skipped, and to emit the resulting domain annotation files. [1] [2] [3] [4] [5]

New wget module:

  • Added a new wget module (modules/nf-core/wget) with process definition, environment, metadata, and tests for downloading files, and registered it in modules.json. [1] [2] [3] [4] [5] [6] [7]

Pipeline and workflow updates:

  • Updated the main workflow and module configuration to include the new MetagRoot annotation step, passing the relevant parameters and configuring process behavior. [1] [2] [3] [4] [5]

Documentation and citation:

  • Modified the citation and bibliography text generation to include MetagRoot in the domain annotation references when used. [1] [2]
  • 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/proteinannotator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (e.g. nf-test test */local --profile=~test,docker for all new local tests).
  • Check for unexpected warnings in debug mode (nf-test test */local --profile=~test,docker,debug).
  • 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).

@angelphanth angelphanth requested a review from vagkaratzas March 13, 2026 16:01
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github-actions Bot commented Mar 13, 2026 •
edited by nf-core-bot
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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: 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 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 63fd565

+| ✅ 217 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-13 16:03:38

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@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas

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