biomaster-workflows

BioMaster: Automated Bioinformatics Workflows

ID: biomedical.genomics.biomaster Version: 1.1.0 Status: Integrated & Downloaded Category: Genomics / Workflow Orchestration

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Overview

BioMaster is a multi-agent system for end-to-end bioinformatics pipelines across multiple omics modalities. It decomposes high-level tasks into reproducible steps with tool-specific parameters and error recovery.

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Supported Workflows

• RNA-seq: QC -> alignment -> quantification -> DEG -> enrichment
• ChIP-seq: QC -> alignment -> peak calling -> motif analysis
• Single-cell: QC -> normalization -> clustering -> annotation
• Hi-C: QC -> alignment -> contact map -> compartment analysis

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Inputs

Field	Type	Notes
config_path	str	YAML config with tool paths and parameters
input_data	str	FASTQ, BAM, or h5ad depending on workflow
workflow	str	rnaseq, chipseq, singlecell, hic

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Outputs

• Standard pipeline outputs (BAM, counts, peak files)
• QC reports and logs
• Summary report with parameters and runtime metadata

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Quick Start

cd repo
pip install -r requirements.txt
python repo/run.py --config repo/config.yaml

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Guardrails

• Always log tool versions and parameters for reproducibility.
• Fail fast on missing reference genomes or index files.
• Require explicit confirmation before deleting intermediate files.

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References

• https://github.com/ai4nucleome/BioMaster