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

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/61428c0675f758f719b65e9d9fc84d/.command.sh
Size: 486 bytes
Task: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX (HCC1395_tumor_vs_HCC1395_BL;manta)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bgzip  --threads 1 -c  HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.ann.vcf > HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.ann.vcf.gz
tabix --threads 1  HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.ann.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX":
    tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS