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Nextflow Pipelines

Build, run, debug and configure Nextflow DSL2 and nf-core data pipelines

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
8 files

What it does

Once installed, the agent can help you run existing Nextflow or nf-core pipelines, write new DSL2 pipeline code, set up configuration for containers and schedulers (such as SLURM or cloud batch), write and run nf-test tests, and diagnose failed or resumed runs. It follows the skill's guidance on pinning versions and using reference files for each task. The skill is a set of instructions and reference documents, so the actual work happens by running the Nextflow tools on your machine or server.

Great for

  • Bioinformaticians or data engineers running nf-core pipelines such as RNA-seq
  • Developers writing or testing Nextflow modules, subworkflows or nf-core-style pipelines
  • Teams moving pipelines between a laptop, an HPC cluster and cloud batch services

Skip it if

  • Users who want a simple script with no workflow engine, since Nextflow adds Java and configuration overhead
  • Anyone running pipelines on sensitive data without reviewing container images, downloads and credentials first, since the skill's commands fetch software and data from the internet
  • Non-technical users without access to a terminal, Java 17-26 or a container engine

Try asking

  • “Run the nf-core/rnaseq test profile with Docker to check my setup, then a real run with my samplesheet”
  • “My Nextflow run failed on SLURM; help me read the log and resume it”
  • “Write a DSL2 process and workflow that aligns FASTQ files and publishes the results”
  • “Set up nf-test tests for this nf-core module”
Step-by-step guide: how to use Nextflow PipelinesInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 8 original files, the MIT licence and an attribution note.

    nextflow.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip nextflow.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip nextflow.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run the small test profile first and check its resource and download needs before a full run; a passing test does not prove scientific accuracy.
  • Pin the Nextflow version and pipeline release with NXF_VER and -r so runs are reproducible.
  • Review the install script and any pipeline's containers and credentials before executing them, especially on shared or sensitive systems.

What's inside

  • references/configuration.md
  • references/containers.md
  • references/developing.md
  • references/language.md
  • references/nf-core-tools.md
  • references/running-pipelines.md
  • references/testing.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.