# Nextflow

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Testing
- License: Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill nextflow -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill nextflow -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill nextflow -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill nextflow -g -a gemini-cli -y`

## Description

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Nextflow

## Overview

Nextflow is a workflow language and runtime for building **reproducible, portable, scalable** data pipelines. It is dominant in bioinformatics but works for any data-heavy computation. nf-core is a community curating production-grade Nextflow pipelines, reusable modules, and the `nf-core` tooling on top of Nextflow.

Key ideas:
- **Dataflow programming**: pipelines are `process` tasks connected by **channels**. Nextflow infers execution order and parallelism from data dependencies, there is no explicit scheduler to write.
- **Write once, run anywhere**: the same pipeline runs locally, on HPC (SLURM, SGE, LSF, PBS), and on cloud (AWS Batch, Google Batch, Azure Batch, Kubernetes) by changing config/profiles, not code.
- **Reproducibility**: per-task containers (Docker/Singularity/Apptainer/Conda/Wave) + `-resume` caching + pinned pipeline revisions.
- **DSL2** is the modern, required syntax: modular `process`/`workflow`/`include` definitions.

This skill covers both **running** existing pipelines and **developing** your own (Nextflow language + nf-core conventions, testing with nf-test, configuration, and deployment).

## When to Use This Skill

Use this skill when the user wants to:
- Run an nf-core or custom Nextflow pipeline, or debug a failing/resuming run.
- Write or modify `.nf` scripts, `nextflow.config`, profiles, or `nextflow_schema.json`.
- Author or test nf-core-style modules/subworkflows (`main.nf`, `meta.yml`, `tests/`, nf-test).
- Configure executors, containers, or resources; scale to HPC or cloud.
- Build a reproducible scientific/bioinformatics workflow (even if "Nextflow" is not named).
- Understand processes, channels, operators, `take`/`emit`, `publishDir`, `ext.args`, meta maps.

## Setup

Nextflow needs **Bash** and **Java 17 or newer** (17, 25 supported). Verify with `java -version`.

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/nextflow/SKILL.md