#!/bin/bash -euo pipefail
extract_aih_qc_metrics.py \
    --metadata dev_rna_experiments_unified_table_2026-05-29.tsv \
    --manifest sample_manifest.tsv \
    --aih-manifest dev_rna_harmonization_latest_2026-06-04.tsv \
    --target-experiments dev_rna_exp0016,cgp_rna_exp0034 \
    --qc-rules qc_rules_default.yaml \
    --metadata-qc-output metadata_qc.tsv \
    --analysis-manifest-output analysis_manifest.tsv \
    --qc-metrics-output aih_qc_metrics.tsv \
    --audit-output aih_qc_extract_audit.tsv

cat <<-END_VERSIONS > versions.yml
"RECALL:EXTRACT_AIH_QC_METRICS":
    python: $(python --version 2>&1 | sed 's/Python //')
    extract_aih_qc_metrics: "1.0.0"
END_VERSIONS