biomaster-workflows

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

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.