#!/bin/bash -Ceuo pipefail
if [ "1" -ne 10 ]; then
    printf '[manta]\nminSomaticScore = 1\n' > manta_override.ini
fi

configManta.py \
    --tumorBam   659_btj-T1-TDNA-1_A23NLJYLT4_2.recalibrated.bam \
    --normalBam  659_btj-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam \
    --reference  Homo_sapiens_assembly38.fasta \
    --runDir     manta \
    --fusionGeneBed foresight_panel_for_manta.bed \
    --maxFusionBinPartners 20 \
    --config manta_override.ini \
    --exome

python manta/runWorkflow.py -m local -j 14

mv manta/results/variants/candidateSmallIndels.vcf.gz     659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.candidate_small_indels.vcf.gz
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi 659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.candidate_small_indels.vcf.gz.tbi
mv manta/results/variants/candidateSV.vcf.gz              659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.candidate_sv.vcf.gz
mv manta/results/variants/candidateSV.vcf.gz.tbi          659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.candidate_sv.vcf.gz.tbi
mv manta/results/variants/somaticSV.vcf.gz                659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.somatic_sv.vcf.gz
mv manta/results/variants/somaticSV.vcf.gz.tbi            659_btj-T1-TDNA-1_A23NLJYLT4_2_vs_659_btj-N1-BDNA-1_B23H3Y2LT3_1.manta_fusion.somatic_sv.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_CALL":
    manta: $( configManta.py --version )
END_VERSIONS