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Bio Prefect Dask Nextflow

Checked
fmschulz·vlatest·data·MIT

This skill orchestrates bioinformatics workflows using Dask and Nextflow for efficient, scalable data processing and analysis.

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 fmschulz/omics-skills --skill bio-prefect-dask-nextflow -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

fmschulz

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 passed all 6 checks. We read its files at one commit and looked for the things that make a skill dangerous to run — not for whether it works.

  • 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 undeclared network calls: passed

    Makes no network calls.

    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.

  • 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.

  • No pipe-to-shell installers: passed

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

  • Pinned to a commit: passed

    Scanned fmschulz/omics-skills at 493585ac4b.

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

Commit
493585ac4b
Manifest
skills/bio-prefect-dask-nextflow/SKILL.md
Scanned
7 files, 472 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.
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About this skill

What it does

This skill combines Prefect, Dask, and Nextflow to orchestrate bioinformatics workflows. It allows for parallelization of tasks within these pipelines, enabling faster processing of large datasets like genomics or proteomics data. The combination facilitates reproducible research by managing dependencies and execution environments.

When to use it

  • Analyzing large-scale genomic sequencing data (e.g., whole genome sequencing).
  • Running complex proteomics workflows involving multiple analysis steps.
  • Reproducing published bioinformatics pipelines for validation or adaptation.
  • Automating the processing of RNA-seq data for gene expression analysis.
  • Building and deploying custom bioinformatics tools as scalable, reproducible workflows.

Key capabilities

  • Prefect workflow orchestration
  • Dask parallel computing
  • Nextflow pipeline execution
  • Scalable data processing
  • Reproducible research pipelines

Example prompts

  • "Run the variant calling pipeline on this FASTQ file."
  • "Execute the RNA-seq differential expression analysis using Dask for faster computation."
  • "Deploy a Nextflow workflow to analyze proteomics data from these raw files."

Tips & gotchas

  • Requires familiarity with Prefect, Dask, and Nextflow concepts.
  • Ensure sufficient computational resources are available for parallel processing with Dask.