#!/bin/bash -Ceuo pipefail
source /opt/conda/etc/profile.d/conda.sh && \
conda activate env_facets && \
run_cnv_facets.R \
-t 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam \
-n 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam \
-o 1029_01S \
-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