PlantAI-dev/skills/wgs-align/SKILL.md

name, description

name	description
wgs-align	Run Stage 03 WGS alignment from the exact successful Stage01 QC and Stage02 index authority Manifests.

WGS alignment

Run only the canonical import-safe entry point:

python -m apps.cli.run_wgs_align \
  --workspace <job-workspace> --job-id <job-id> --prefix <prefix> \
  --qc-manifest <workspace/final/prefix.wgs_qc.manifest.json> \
  --index-manifest <workspace/final/prefix.wgs_index.manifest.json> \
  --bwa-mem2 <bwa-mem2> --samtools <samtools> \
  --threads <positive-int> --max-jobs <positive-int> --platform illumina

Do not supply read, reference, or index paths directly and do not scan directories. The CLI resolves every input from the two authority Manifests and fails closed on producer, identity, role, immutable-path, size, hash, sample, or component drift. Success requires a sorted BAM, matching BAI, diagnostic alignment log, exact read group sample identity, and input/output sample-set conservation for every sample.