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Biomaster workflows

Skill FridrichMethod/awesome-skills/skills/biomaster-workflows

Pipeline maestroFrom its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill biomaster-workflows

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

2 things to look at

  • no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.
  • 13 stars13 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its file declares

Copied from the file, not written here

The file declares its own license as MIT. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

1.9 KB, 370 tokens by cl100k_base, as published. Nobody here has run it

<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

BioMaster Workflows

Orchestrate BioMaster’s multi-agent pipelines (RNA-seq, ChIP-seq, single-cell, Hi-C) using the provided configs and repos to deliver reproducible outputs.

Workflow

  1. Config prep: Populate YAML with tool paths, reference genomes, and workflow selection (rnaseq, chipseq, singlecell, hic).
  2. Environment: cd repo && pip install -r requirements.txt (or container) prior to running.
  3. Launch: python repo/run.py --config repo/config.yaml (or chosen config) and monitor progress.
  4. Error recovery: Let BioMaster agents retry failing stages; review logs for missing reference/index files.
  5. Output packaging: Collect BAMs/counts/peaks + QC + narrative summary of parameters and runtimes.

Guardrails

  • Fail fast when reference files or indices are absent to avoid wasted compute.
  • Record tool versions for every stage (alignment, quantification, etc.).
  • Require confirmation before deleting intermediates or rerunning destructive steps.

References

  • Full workflow descriptions, supported modalities, and repo links reside in README.md.
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it: 99 files

953.6 KB alongside SKILL.md, 59 of them executable

repo/

59 more files not listed here. See all 99 in the repository.

Keep looking

Skills are one crate of 325,949. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.