Bio Reads QC Mapping

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Instructions

Tool guides and versions: docs/README.md.

1. Parse and validate sample_sheet.tsv against schemas/sample-sheet.schema.json. Use the executable driver for both planning and restartable execution:

   uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \
     sample_sheet.tsv --out results/bio-reads-qc-mapping
   # Inspect run_manifest.json, then execute the same plan:
   uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \
     sample_sheet.tsv --out results/bio-reads-qc-mapping --execute