nf-meta: metapipeline representation, editor, and runner

A reproducible representation for Nextflow metapipelines — chains of nf-core/Nextflow pipeline and module runs — with an interactive browser-based editor and a CLI validator/runner.

This is a beta version: things can be unstable and change.

📖 Documentation — installation, quickstart, the full config reference, and the API reference.

Find a growing collection of examples in the dedicated showcase repository.

Representation

A metapipeline is a .yaml file. The most important keys are:

• config_version — allows the representation to change over time without breaking
• workflows — the nextflow / nf-core pipeline runs. The flow from workflow to workflow is described by each workflow's own from: key
• globals — settings that apply to all workflows

config_version: 0.3.0
globals:
  nextflow_version: "25.10"
workflows:
  n01:
    name: nf-core/fetchngs
    version: 1.12.0
    params:
      input: fetchngs-ids.csv
      outdir: out_fetchngs
      nf_core_pipeline: rnaseq
      nf_core_rnaseq_strandedness: auto
  n02:
    from: n01
    name: nf-core/rnaseq
    version: 3.14.0
    params:
      input: ${n01:params:outdir}/samplesheet/samplesheet.csv
      genome: GRCh38
      outdir: out_rnaseq

Fields can reference another workflow's own params, so you write input: ${n01:params:outdir}/samplesheet/samplesheet.csv instead of hardcoding input: fetchngs_out/samplesheet/samplesheet.csv.

See the config reference for every key, and cross-workflow references for the full ${...} syntax.

Runners

Currently:

• Python runner — wraps nextflow commands, executes in DAG order.

Planned:

1. nf-cascade runner — convert the config into one daisy-chained Nextflow script.
2. Seqera Platform runner — start and monitor locally, calling a Platform instance's API with run parameters to handle running Nextflow.
3. Meta-pipeline runner — compile the config into a new monolithic Nextflow project that imports the required workflows, for the most efficient orchestration and graceful error handling.

Runners are pluggable — see the runner docs to write your own.

Install from PyPI

# with pip
pip install nf-meta

# with uv
uv add nf-meta

See the docs for the development setup, the editor, and the full API reference.