By 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.