Selection Report — the founding twenty
Date: 2026-08-15 · Method: GitHub API data + snakemake catalog, scored by a selection committee agent against pre-registered criteria, then reviewed by the maintainer.
This report documents how the first twenty entries in the catalog were chosen. The catalog has since opened to original workflows and community submissions — see Curation & ratings.
Method
Data was collected from the live GitHub API on 2026-08-15:
- nf-core:
org:nf-core fork:false archived:false, sorted by stars (30 analysis pipelines after excluding infrastructure repos: modules 424★, tools 319★, test-datasets 164★, configs 110★, website 98★). - Snakemake: GitHub search
snakemake workflow in:name,description stars:>30merged with the official workflows.snakemake.org catalog listing.
Criteria (pre-registered weights)
| Criterion | Weight | Definition |
|---|---|---|
| Usage & adoption | 40% | GitHub stars; snakemake-catalog presence |
| Maintenance health | 20% | pushed_at within ~18 months, not archived |
| Portability | 25% | default-parameters main path ≈ 5–45 rules, expressible in oxo-flow |
| Domain diversity | 15% | library-wide coverage across omics domains |
Fidelity scope for every port: the default-parameters main execution path is replicated 100% (tools, versions, command logic); optional/alternate paths are documented as exclusions in each repo's README fidelity table.
Selection (20)
| Port repo | Source (engine) @ tag | ★ | Domain | Rules† | Verify |
|---|---|---|---|---|---|
| oxo-flow-rnaseq | nf-core/rnaseq @ 3.26.0 | 1349 | bulk RNA-seq | 14 | ✓ |
| oxo-flow-sarek | nf-core/sarek @ 3.10.0 | 592 | WGS/WES germline | 12 | ✓ |
| oxo-flow-scrnaseq | nf-core/scrnaseq @ 4.2.0 | 349 | single-cell RNA-seq | 8 | |
| oxo-flow-mag | nf-core/mag @ 5.5.0 | 314 | metagenomics | 10 | ✓ |
| oxo-flow-ampliseq | nf-core/ampliseq @ 2.18.0 | 256 | amplicon (16S/ITS) | 8 | |
| oxo-flow-chipseq | nf-core/chipseq @ 2.1.0 | 242 | ChIP-seq | 10 | ✓ |
| oxo-flow-nanoseq | nf-core/nanoseq @ 3.1.0 | 228 | nanopore long-read | 6 | |
| oxo-flow-atacseq | nf-core/atacseq @ 2.1.2 | 226 | ATAC-seq | 9 | |
| oxo-flow-eager | nf-core/eager @ 2.5.3 | 212 | ancient DNA | 12 | ✓ |
| oxo-flow-fetchngs | nf-core/fetchngs @ 1.12.0 | 200 | fetch/QC utility | 6 | |
| oxo-flow-methylseq | nf-core/methylseq @ 4.2.0 | 197 | WGBS methylation | 8 | |
| oxo-flow-viralrecon | nf-core/viralrecon @ 3.0.0 | 167 | viral genomics | 12 | ✓ |
| oxo-flow-rnaseq-star-deseq2 | snakemake-workflows/rna-seq-star-deseq2 @ v3.1.1 | 370 | bulk RNA-seq | 7 | |
| oxo-flow-snparcher | harvardinformatics/snparcher @ v2.2 | 95 | non-model variant calling | 9 | |
| oxo-flow-varlociraptor | snakemake-workflows/dna-seq-varlociraptor @ v6.10.0 | 90 | small & structural variants | 8 | |
| oxo-flow-enrichment | epigen/enrichment_analysis @ v3.0.1 | 77 | functional enrichment | 6 | |
| oxo-flow-unsupervised | epigen/unsupervised_analysis @ v4.0.2 | 67 | post-analysis statistics | 7 | |
| oxo-flow-genome-tracks | epigen/genome_tracks @ v2.0.5 | 57 | genome-browser tracks | 6 | |
| oxo-flow-mixscape | epigen/mixscape_seurat @ v2.0.3 | 56 | CRISPR perturbation | 7 | |
| oxo-flow-bgcflow | NBChub/bgcflow @ v1.1.2 | 55 | biosynthetic gene clusters | 6 |
† Estimated rule count of the default main path. ✓ = fidelity verification agent assigned.
Notable non-selections (and why)
- snakemake-workflows/dna-seq-gatk-variant-calling (267★) — the canonical GATK best-practices tutorial, but unmaintained since 2023-06; maintenance criterion (20%) disqualified it, and variant-calling is covered by sarek/snparcher/varlociraptor.
- Hoohm/dropSeqPipe (149★) and snakemake-workflows/single-cell-rna-seq (107★) — stale (2023 / 2022); single-cell covered by scrnaseq.
- maxplanck-ie/snakepipes (407★) — actively maintained but a collection of ~20 pipelines, not one workflow; unsuitable as a single template repo.
- snakemake/snakemake (2847★) — the engine itself, not a workflow.
- csoneson/ARMOR (168★) — RNA-seq preprocessing is covered by both rnaseq ports.
Domain coverage
bulk RNA-seq (rnaseq, rnaseq-star-deseq2) · single-cell (scrnaseq) · WGS/WES (sarek) · metagenomics + amplicon (mag, ampliseq) · epigenetics ChIP/ATAC/methyl (chipseq, atacseq, methylseq) · viral (viralrecon) · long-read (nanoseq) · ancient DNA (eager) · variant calling non-model/SV (snparcher, varlociraptor) · microbial natural products (bgcflow) · CRISPR perturbation (mixscape) · post-analysis (enrichment, unsupervised, genome-tracks) · fetch/QC (fetchngs).
Known gap: proteomics — the only strong candidate (nf-core/proteinfold) has a GPU-heavy few-rule default path with poor portability value; left for a future round.
Chair review notes
- All 20 sources are MIT-licensed, none archived, every one pushed within ~13 months of the selection date.
- All tags/commit SHAs in
pipeline-specs.jsonwere fetched live from the GitHub API at selection time — no invented versions. - The snakemake half draws 4/8 entries from the maintained MrBiomics (epigen) suite: provenance is concentrated, but the four cover four distinct domains and each is catalog-listed and actively maintained. Accepted with this note.
- The 6 highest-complexity ports (rnaseq, sarek, viralrecon, eager, mag, chipseq) carry a mandatory fidelity-verification stage against upstream source.