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

configManta.py \
    --tumorBam   COLO829_c_0001_gDNA_0001_B23H2NLLT4_10.recalibrated.bam \
    --normalBam  COLO829BL_c_01_gDNA_0001_A237FLHLT3_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     COLO829_tumor_10pct_rep2.manta_fusion.candidate_small_indels.vcf.gz
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi COLO829_tumor_10pct_rep2.manta_fusion.candidate_small_indels.vcf.gz.tbi
mv manta/results/variants/candidateSV.vcf.gz              COLO829_tumor_10pct_rep2.manta_fusion.candidate_sv.vcf.gz
mv manta/results/variants/candidateSV.vcf.gz.tbi          COLO829_tumor_10pct_rep2.manta_fusion.candidate_sv.vcf.gz.tbi
mv manta/results/variants/somaticSV.vcf.gz                COLO829_tumor_10pct_rep2.manta_fusion.somatic_sv.vcf.gz
mv manta/results/variants/somaticSV.vcf.gz.tbi            COLO829_tumor_10pct_rep2.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