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Add snpclustering subworkflow#11059

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dbaku42 wants to merge 1 commit intonf-core:masterfrom
dbaku42:add/snpclustering
Open

Add snpclustering subworkflow#11059
dbaku42 wants to merge 1 commit intonf-core:masterfrom
dbaku42:add/snpclustering

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@dbaku42 dbaku42 commented Mar 26, 2026

Description

This PR adds the snpclustering subworkflow for end-to-end unsupervised clustering of genomic samples directly from multi-sample VCF files.

Features

  • Variant filtering (MAF + missingness) with bcftools/filter
  • LD pruning with plink2/indeppairwise
  • Export pruned VCF with plink2/recodevcf
  • PCA with flashpca2

The subworkflow was developed in relation to the accepted nf-core proposal for the consepopgen pipeline.

Related to:

Checklist

  • nf-core subworkflows lint snpclustering passed
  • nf-core subworkflows test snpclustering passed
  • Follows nf-core subworkflow conventions

Closes # (no specific issue)

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