> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# nextflow — AI agent skill for life sciences

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

# `nextflow`

> 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.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** Apache-2.0 · **Version:** 1.2

## Install

```bash theme={null}
npx research-agent-skills install nextflow
npx skills add KalarisLabs/research-agent-skills --skill nextflow
```

## When to use it

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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/nextflow/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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