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Bio Workflow Management Nextflow Pipelines

Listed
gptomics·vlatest·devops·MIT

Automates and optimizes complex genomic bio workflows using Nextflow pipelines within a DevOps environment.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add gptomics/bioskills --skill bio-workflow-management-nextflow-pipelines --full-depth -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

gptomics

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 2 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 1 host that is neither well-known infrastructure nor declared in the skill's frontmatter: get.nextflow.io.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    get.nextflow.ioundeclared

    What it found

    • workflow-management/nextflow-pipelines/usage-guide.md:11contacts get.nextflow.io
      curl -s https://get.nextflow.io | bash

  • No pipe-to-shell installers: failed

    Runs code fetched at install time in 1 place.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

    What it found

    • workflow-management/nextflow-pipelines/usage-guide.md:11remote script piped into a shell
      curl -s https://get.nextflow.io | bash

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • Pinned to a commit: passed

    Scanned gptomics/bioskills at d91ed3d563.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
d91ed3d563
Manifest
workflow-management/nextflow-pipelines/SKILL.md
Scanned
2 files, 311 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill enables the automation and orchestration of bioinformatics workflows using Nextflow pipelines. It allows users to define, execute, and manage complex analyses involving genomic data processing, variant calling, or other downstream tasks. The skill streamlines repetitive processes, ensures reproducibility, and facilitates collaboration among researchers.

When to use it

  • Running a standard genomics analysis pipeline on a large dataset.
  • Reproducing published bioinformatics results by executing the associated Nextflow workflow.
  • Developing and testing new bioinformatics workflows before deployment in a production environment.
  • Automating daily or weekly data processing tasks for genomic surveillance projects.

Key capabilities

  • Nextflow pipeline execution
  • Workflow definition using Nextflow DSL
  • Parameterization of pipelines through command-line arguments
  • Data input and output management within workflows
  • Reproducible analysis results

Example prompts

  • "Run the 'variant_calling' Nextflow pipeline with these sample files."
  • "Execute the 'rnaseq_analysis' workflow, setting the number of threads to 8."
  • "Show me the logs for the last execution of the 'atac_seq' pipeline."

Tips & gotchas

  • Requires familiarity with Nextflow syntax and concepts.
  • Ensure that all necessary dependencies (software, databases) are available in the environment where the skill is executed.