#!/bin/bash -Ceuo pipefail
score_chip_variants.py \
    --vcf Sig_18_Blood.readcount_annotated.vcf.gz \
    --output Sig_18_Blood.scored.vcf.gz \
    --blacklist cohort_blacklist.bed.gz \
    --cosmic-heme cosmic_heme.tsv.gz \
    --gene-tiers gene_tiers.tsv

tabix -p vcf Sig_18_Blood.scored.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS":
    score_chip_variants: $(score_chip_variants.py --version 2>&1 || echo "1.0.0")
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS