#!/bin/bash -Ceuo pipefail
source /opt/conda/etc/profile.d/conda.sh && \
conda activate env_facets && \
run_cnv_facets.R \
-t FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam \
-n reference-NA12878.bam \
-o positive_somatic_control_1 \
-vcf dbsnp_146.hg38.vcf.gz \
-genes Homo_sapiens.GRCh38.110.gtf.gz \
cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC: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