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Building and debugging Nextflow pipelines v1.0.0

Use this resource to write, run and debug Nextflow and nf-core pipelines

New

  • 324 downloads
  • 187 likes
  • 177 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install nextflow-pipeline-development

With no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.

First time: connect the CLI with

npx --yes palatekit@latest login

The agent writes processes and channels, sets configuration and containers, then diagnoses failed or resumed runs. You get a structured pipeline, its configuration and test steps.

Mostly picked by

Updated November 2, 2026

Card for the “Building and debugging Nextflow pipelines” skill

Details

Works in
Install guides
Generates with
Your agent's model
Licence
Apache-2.0

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What you get

  • SKILL.md: installation, work modes and quick start
  • references/: language, configuration, containers, testing, nf-core tools and execution

Good fit for

  • Your analysis script must run on a SLURM cluster
  • A Nextflow run failed and needs to resume

Not for

    Tags

    • Nextflow
    • pipeline
    • nf-core

    About

    You say

    “Add a quality control process to my Nextflow pipeline and configure Docker.”

    Card for the “Building and debugging Nextflow pipelines” skill

    Skill published by k-dense-ai under the Apache-2.0 license, delivered in its original version.

    Show more

    How to use it

    1. Install the skill in your agent's skills folder
    2. Ask your agent to write, run and debug Nextflow and nf-core pipelines
    3. Review and adjust the result

    Content preview

    Files

    • LICENSE1.1 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/configuration.md12.9 KB
    • references/containers.md5.4 KB
    • references/developing.md16.9 KB
    • references/language.md18.5 KB
    • references/nf-core-tools.md7 KB
    • references/running-pipelines.md8.1 KB
    • references/testing.md9.2 KB
    • SKILL.md14.8 KB

    Origin and licence

    Listed unmodified

    Author
    k-dense-ai
    Source
    github.com/k-dense-ai/scientific-agent-skills/tree/5f2bc0341354fd5590aef76a533ada1e1e5b4e62/skills/nextflow
    Licence
    Apache-2.0

    Notice

    « nextflow » (k-dense-ai, Apache-2.0) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.

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