.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (Sig_18_Blood;tnseq)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/cdfa01d584b6fcf9df8fb6d8095b41/.command.sh
Size: 512 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (Sig_18_Blood;tnseq)
Attempt

Content

#!/bin/bash -Ceuo pipefail
snpEff \
    -Xmx13107M \
    GRCh38.105 \
    -nodownload -canon -v \
    -csvStats Sig_18_Blood.tnseq_tumor_only.filtered_snpEff.csv \
    -dataDir ${PWD}/GRCh38.105 \
    Sig_18_Blood.tnseq_tumor_only.filtered.vcf.gz \
    > Sig_18_Blood.tnseq_tumor_only.filtered_snpEff.ann.vcf

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