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famosab
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famosab
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Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.
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We also want a snapshot here (look at other subworkflows)
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The test now passes with direct nf-test. The failure with nf-core subworkflows test is due to a temporary missing Wave container for the plink2/vcf module (manifest unknown). The logic and snapshot are correct.
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Check for each module if they still export the versions I think at least bcftools/filter does not anymore
| FLASHPCA2 ( PLINK2_RECODE_VCF.out.vcf ) | ||
| versions = versions.mix(FLASHPCA2.out.versions.first()) | ||
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| // TODO: qui aggiungeremo KMeans/DBSCAN/plot quando creeremo i moduli local |
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Is there still something to add?
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Thank you for your comment @famosab .
You’re absolutely right — the clustering components (KMeans, DBSCAN), internal validation metrics (Silhouette, Calinski–Harabasz, Davies–Bouldin), non-linear embeddings (t-SNE/UMAP), and the final HTML report still need to be integrated.
These features are already implemented in the original pipeline (https://github.com/dbaku42/nf-core-snpclustering). I intentionally left them out of this PR to keep the subworkflow minimal and easier to review.
I’m happy to proceed in either of the following ways:
- Include all these components directly in this PR (my preferred option), or
- Add them in a dedicated follow-up PR immediately after this one is merged.
Please let me know which approach you’d prefer.
Thanks again!
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
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Description
This PR adds the
snpclusteringsubworkflow for end-to-end unsupervised clustering of genomic samples directly from multi-sample VCF files.Features
bcftools/filterplink2/indeppairwiseplink2/recodevcfflashpca2The subworkflow was developed in relation to the accepted nf-core proposal for the
consepopgenpipeline.Related to:
Checklist
nf-core subworkflows lint snpclusteringpassednf-core subworkflows test snpclusteringpassedCloses # (no specific issue)