#!/bin/bash -Ceuo pipefail
source /opt/conda/etc/profile.d/conda.sh && \
conda activate env_facets && \
run_cnv_facets.R \
    -t HCC1395_tumor.recalibrated.bam \
    -n HCC1395_BL.recalibrated.bam \
    -o HCC1395_tumor_vs_HCC1395_BL \
    -vcf dbsnp_146.hg38.vcf.gz \
    -genes Homo_sapiens.GRCh38.110.gtf.gz \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS":
    facets: $(Rscript -e 'packageVersion("facets")' 2>/dev/null | cut -f2 -d  ' ' | iconv -f utf-8 -t ascii//translit || echo "unknown")
END_VERSIONS