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Get started — run your first workflow in 10 minutes

The catalog is to be used, not just read: every workflow page ships real commands, a live semantic walkthrough, and parameters you can copy. This page walks one full round trip — install the engine, pick a workflow, preview the plan, run it, read the report.

1. Install the engine

Pick one:

# Binary (fastest): grab the latest release for your platform
#   https://github.com/Traitome/oxo-flow/releases

# Or via Cargo
cargo install oxo-flow-cli

# Or via Conda
conda install -c bioconda oxo-flow-cli

Check it:

oxo-flow --version
oxo-flow --help

2. Pick a workflow — and understand it first

Every card's Semantic overview on the workflow page tells you what the pipeline does before you run it, in plain language — each step named with its real rule. Start with RNA-seq: STAR alignment, DESeq2 differential expression and QC (oxo-flow-rnaseq-star-deseq2): a full RNA-seq differential-expression pipeline with built-in test data and a live-tested rating.

3. Preview — or run straight from GitHub

You can skip cloning entirely — the engine fetches the repo itself:

oxo-flow run gh:oxo-flow-community/oxo-flow-rnaseq-star-deseq2

It checks the repo out under .oxo-flow/repos/<name> and keeps outputs in your current directory. When you want to inspect first, clone for real and preview:

git clone https://github.com/oxo-flow-community/oxo-flow-rnaseq-star-deseq2.git
cd oxo-flow-rnaseq-star-deseq2

Never run blind: preview the exact plan first — rules, samples, instances, resources:

oxo-flow validate main.oxoflow
oxo-flow dry-run main.oxoflow

The workflow ships a built-in sample group (its [[sample_groups]]), so the plan is fully materialized without extra input files.

4. Run

oxo-flow run main.oxoflow

The executor prints every step as it goes; tracing goes to stderr, so the terminal stays clean. Wildcards like {sample} expand per sample, instances run with environment-pinned tools, and a checkpoint lets a failed run resume with --resume.

5. Read the results

  • results/ — count matrices, DESeq2 tables, QC reports (see the workflow's README for the layout).
  • oxo-flow status / oxo-flow inspect <run-dir> — what ran, what awaits a retry, resource usage.

Where to go next