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Reproducible bioinformatics pipelines v1.0.0

Use this resource to build a reproducible bioinformatics pipeline

New

  • 550 downloads
  • 217 likes
  • 230 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install bioinformatics-pipeline-workflows

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 helps you build and maintain bioinformatics pipelines with Nextflow, Snakemake or WDL/Cromwell, with container orchestration and reproducibility practices. You get a pipeline structure and the mistakes to avoid at scale.

Mostly picked by

Updated November 2, 2026

Card for the “Reproducible bioinformatics 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: rules for using the references
  • references/patterns.md: workflow and container models
  • references/sharp_edges.md: scale and reproducibility errors

Good fit for

  • You process sequences through steps that must chain and reproduce
  • Your pipeline runs on one machine and must move to a cluster

Not for

    Tags

    • bioinformatics
    • nextflow
    • snakemake
    • pipeline

    About

    You say

    “Turn my RNA-seq analysis scripts into a Nextflow pipeline that runs in containers.”

    Card for the “Reproducible bioinformatics pipelines” skill

    Skill published by omer-metin 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 build a reproducible bioinformatics pipeline
    3. Review and adjust the result

    Content preview

    Files

    • LICENSE10.1 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/patterns.md14.1 KB
    • references/sharp_edges.md7.9 KB
    • references/validations.md3.4 KB
    • SKILL.md1.1 KB

    Origin and licence

    Listed unmodified

    Author
    omer-metin
    Source
    github.com/omer-metin/skills-for-antigravity/tree/e8dcf4e8737921a10088bd5c9eb65e81f74c051f/skills/bioinformatics-workflows
    Licence
    Apache-2.0

    Notice

    « bioinformatics-workflows » (omer-metin, Apache-2.0) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.

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