Add metagroot domain annot#90
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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. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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vagkaratzas
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Mar 30, 2026
| params.skip_nmpfams, | ||
| params.nmpfams_db, | ||
| params.nmpfams_latest_link, | ||
| params.metagroot_db, |
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I think you forgot to pass the skip flag and the sequence of passed parameters got messed up a bit :D
See end-to-end snapshot failure -probably because of this lil buddy not being here
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PR checklist
Closes #80
This pull request adds support for annotating protein domains using the MetagRoot (MROOT) database to the pipeline. It introduces new configuration parameters, updates documentation and citations, and adds a new
wgetmodule for downloading external resources. The most important changes are grouped below.MetagRoot (MROOT) integration:
skip_mroot,mroot_db,mroot_latest_link) to support domain annotation with the MetagRoot database innextflow.config,test.config, andnextflow_schema.json. These allow users to enable/disable MROOT annotation, specify a local database, or download the latest version. [1] [2] [3]main.nfandconf/modules.configto include new processes for downloading and searching the MROOT database, mirroring the existing setup for other domain databases. [1] [2] [3]New wget module:
wgetmodule (modules/nf-core/wget/) with its process definition, environment, metadata, and comprehensive tests and snapshots. This module is used for downloading external resources such as the MROOT database. [1] [2] [3] [4] [5] [6] [7]Documentation and citation updates:
nf-core/proteinannotator. [1] [2]These changes collectively enable and document support for the MetagRoot database in the protein annotation pipeline, improve reproducibility, and enhance the pipeline's flexibility for users.
nf-core pipelines lint).nf-test test */local --profile=~test,dockerfor all new local tests).nf-test test */local --profile=~test,docker,debug).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).