How do I install the Biomaster Workflows skill?

Run npx skillmds@latest add biotender-max/biomaster-workflows in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Biomaster Workflows skill do?

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Is Biomaster Workflows safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Biomaster Workflows?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Biomaster Workflows free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Biomaster Workflows?

BioTender-max (@biotender-max) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Biomaster Workflows by biotender-max

Name: Biomaster Workflows
Author: BioTender-max

File contents

name: biomaster-workflows description: Pipeline maestro keywords: - workflows - RNAseq - ChIPseq - automation - YAML measurable_outcome: Execute a configured pipeline end-to-end (including QC report + summary) within 24 hours of receiving inputs, logging every tool/parameter. license: MIT metadata: author: BioMaster Team version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - read_file

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

Config prep: Populate YAML with tool paths, reference genomes, and workflow selection (rnaseq, chipseq, singlecell, hic).
Environment: cd repo && pip install -r requirements.txt (or container) prior to running.
Launch: python repo/run.py --config repo/config.yaml (or chosen config) and monitor progress.
Error recovery: Let BioMaster agents retry failing stages; review logs for missing reference/index files.
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.

---name: biomaster-workflowsdescription: ---name: biomaster-workflowsdescription: Pipeline maestrokeywords: - workflows - RNAseq - ChIPseq - automation - YAMLmeasurable_outcome: Execute a configured pipeline end-to-end (including QC report + summary) within 24 hours of receiving inputs, logging every tool/parameter.license: MITmetadata: author: BioMaster Team version: "1.0.0"compatibility: - system: Python 3.9+allowed-tools: - run_shell_command - read_file---# BioMaster WorkflowsOrchestrate BioMaster’s multi-agent pipelines (RNA-seq, ChIP-seq, single-cell, Hi-C) using the provided configs and repos to deliver reproducible outputs.## Workflow1. **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`.

Frequently asked questions

Biomaster Workflows