New module: clustering#11337
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* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add umicollapse * initial clippy module commit * find working test data * complete test * prettier * add a doi * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * remove umicollapse from pytest * rename gtf to include that its from gencode * add test for clippy intergenic mode * remove quay.io
* initial trycycler subsample commit * Update modules/nf-core/trycycler/subsample/main.nf to resolve issue with nf-test and empty gzipped files Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * addressing comments on initial commit, fixed version number, added stub tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
…index files (nf-core#10319) * Update modules * Fix meta * Update samtools stub
module update version
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add umicollapse * initial clippy module commit * find working test data * complete test * prettier * add a doi * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * remove umicollapse from pytest * rename gtf to include that its from gencode * add test for clippy intergenic mode * remove quay.io
* initial trycycler subsample commit * Update modules/nf-core/trycycler/subsample/main.nf to resolve issue with nf-test and empty gzipped files Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * addressing comments on initial commit, fixed version number, added stub tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
…index files (nf-core#10319) * Update modules * Fix meta * Update samtools stub
module update version
- Added flashpca module using custom container ghcr.io/dbaku42/flashpca:2.0 - Fixed file handling for PLINK inputs inside Docker (cp -L + fixed basename) - Updated nf-test to use proper input tuple - Test now passes with --profile docker
…ate environment/meta files - Added containerOptions '--entrypoint ""' to fix argument parsing in Docker - Separated environment.yml (Conda config only) from meta.yml (module documentation) - Hardcoded version to 2.0 for snapshot stability - Fixed dependencies list in environment.yml to prevent linting TypeError
- Remove name field from environment.yml - Fix meta.yml output structure to match schema - Update versions output to tuple with meta for topic compatibility
…abling autoMounts - Add tests/config/nextflow.config with Docker profile - Update tests/main.nf.test - Improve container declaration and version capture in main.nf - Address mount parsing error on GitHub Actions
Performs KMeans or DBSCAN clustering on PLINK2 --pca .eigenvec files. - Supports both KMeans and DBSCAN - Uses conda environment - Includes nf-test with snapshot testing
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- Updated import path from local to nf-core/clustering - Removed custom container reference for now
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May 13, 2026 20:49
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Description
New module:
clusteringPerforms KMeans or DBSCAN clustering on principal components from PLINK2
--pca(.eigenvecfile).Features
kmeansanddbscanalgorithms via parameterscondaenvironment (environment.yml)*_clusters.csv) and metadata (*_clustering_info.json)nf-testcoverage (normal + stub test)Author
Checklist
nf-core modules lint clustering→ passednf-core modules test clustering→ passed (module only)snpclusteringstill uses custom container (will be updated separately)Closes # (if you have an issue)
This PR adds a new standalone module for population clustering.