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OxO Flow Community

Catalogue of oxo-flow Pipelines

oxo-flow-community

The community catalog of oxo-flow workflows — curated, rated, and ready to run.

Browse the catalog →

  • ⇄ Official ports — verified migrations of the pipelines the field already trusts (nf-core, Snakemake): same tools, same versions, same commands, per-rule fidelity tables.
  • ✦ Original workflows — designed for oxo-flow from the start.
  • ♺ Community listings — any public repository can join the catalog via pull request; the catalog links to it, nothing moves.

Ratings are evidence-based:

  • ✔ Live-tested — the workflow was run end-to-end on a reference server with minimal real or synthetic data: every rule completed, exit 0, report snapshot written.
  • ★ Verified — fidelity-reviewed migration, pins tool versions, passes validate + dry-run in CI.
  • ☆ Community — listed via pull request, not yet reviewed.

See the live-testing practice for the methodology.

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© 2026 oxo-flow-community · Apache-2.0

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  1. oxo-flow-scrnaseq oxo-flow-scrnaseq Public

    Single-cell RNA-seq (10x / DropSeq / SmartSeq) — oxo-flow port of nf-core/scrnaseq

    Python

  2. oxo-flow-sarek oxo-flow-sarek Public

    WGS/WES germline and somatic variant calling — oxo-flow port of nf-core/sarek

    Shell

  3. oxo-flow-rnaseq-star-deseq2 oxo-flow-rnaseq-star-deseq2 Public

    RNA-seq with STAR and DESeq2 (snakemake catalog flagship) — oxo-flow port of snakemake-workflows/rna-seq-star-deseq2

    R

  4. oxo-flow-atacseq oxo-flow-atacseq Public

    ATAC-seq peak calling and QC — oxo-flow port of nf-core/atacseq

    R

  5. oxo-flow-ampliseq oxo-flow-ampliseq Public

    Amplicon sequencing (16S/ITS) with DADA2 and QIIME2 — oxo-flow port of nf-core/ampliseq

    R

  6. oxo-flow-community.github.io oxo-flow-community.github.io Public

    Official website of oxo-flow-community — searchable catalog of workflow by oxo-flow (https://github.com/Traitome/oxo-flow)

    Python 1

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