.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (HCC1395_BL;sentieon_haplotyper_rf)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/35d3a28d233ac5b9da8ec1f8b7e9ea/.command.sh
Size: 364 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (HCC1395_BL;sentieon_haplotyper_rf)
Attempt

Content

#!/bin/bash -Ceuo pipefail
vcftools \
    --gzvcf HCC1395_BL.deconflicted_germline.vcf.gz \
    --out HCC1395_BL.deconflicted_germline \
    --TsTv-by-qual \
     \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL":
    vcftools: $(echo $(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS