#!/bin/bash -Ceuo pipefail
snpEff \
    -Xmx13107M \
    GRCh38.105 \
    -nodownload -canon -v \
    -csvStats HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv \
    -dataDir ${PWD}/GRCh38.105 \
    HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann.vcf.gz \
    > HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.ann.vcf

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF":
    snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS