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Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ff4e6c5f100b75d4378c72d7091ad2/.command.sh
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1.7 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_CALL (1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1)
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#!/bin/bash -Ceuo pipefail
if [ "1" -ne 10 ]; then
    printf '[manta]\nminSomaticScore = 1\n' > manta_override.ini
fi

configManta.py \
    --tumorBam   1173_HOB-T1-TDNA-01_B23MHVMLT4_1.recalibrated.bam \
    --normalBam  1173_HOB-N1-BDNA-01_B23L5TMLT4_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     1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1.manta_fusion.candidate_small_indels.vcf.gz
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi 1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1.manta_fusion.candidate_small_indels.vcf.gz.tbi
mv manta/results/variants/candidateSV.vcf.gz              1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1.manta_fusion.candidate_sv.vcf.gz
mv manta/results/variants/candidateSV.vcf.gz.tbi          1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1.manta_fusion.candidate_sv.vcf.gz.tbi
mv manta/results/variants/somaticSV.vcf.gz                1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_1.manta_fusion.somatic_sv.vcf.gz
mv manta/results/variants/somaticSV.vcf.gz.tbi            1173_HOB-T1-TDNA-01_B23MHVMLT4_1_vs_1173_HOB-N1-BDNA-01_B23L5TMLT4_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