.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (HCC1395_tumor_vs_HCC1395_BL;manta)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/b7efc3d7497939d9fffe5c3fd47fe3/.command.sh
Size: 544 bytes
Task: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (HCC1395_tumor_vs_HCC1395_BL;manta)
Attempt

Content

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