#!/bin/bash -Ceuo pipefail
sentieon driver -r Homo_sapiens_assembly38.fasta \
 \
--algo TNfilter \
--tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --max_event_count 5 \
-v HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz \
 --contamination HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv  \
--tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments \
--orientation_priors HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv \
HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS