#!/bin/bash -euo pipefail
# The Wave image (htslib_pysam_numpy_scipy) does not bundle scikit-learn,
# which VariantFilter needs to unpickle the RF model. Install it inline
# until the container is rebuilt with sklearn included.
python3 -m pip install --quiet --no-cache-dir scikit-learn joblib

nipt_score_vcf.py \
    --vcf 52943-ND0958_maternal.vcf \
    --bam 52943-ND0958_maternal.dedup.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --rf-model indel_v6_lofo_hp6.pkl \
    --output 52943-ND0958_maternal.indel.scored.vcf \
    --sample-index 0 \
    --rf-min-confidence 0.5 \
    --model-version indel \
    --fetal-fraction 0.0 \
    --default-af 0.5 \
    --gnomad gnomad_af.tsv.gz \