#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 12 \
    -r Homo_sapiens_assembly38.fasta \
     \
    -i 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam \
    --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed \
    --algo TNhaplotyper2 \
    --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-N1-BDNA-1_B23KGCJLT4_1 \
    --call_germline_sites \
    --germline_vcf af-only-gnomad.hg38.vcf.gz \
    --pon pon_tnseq_42_curated_v4.vcf.gz \
    1029_11H.tnseq.vcf.gz \
    --algo OrientationBias --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 1029_11H.tnseq.orientation_data.tsv \
    --algo ContaminationModel --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_11H.tnseq.segments 1029_11H.tnseq.contamination_data.tsv

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS