.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (custom_Sig_18_tumor_normal;strelka)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/32fe73e3c8ddbfc83425ee7f5602c5/.command.sh
Size: 398 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (custom_Sig_18_tumor_normal;strelka)
Attempt

Content

#!/bin/bash -Ceuo pipefail
vcftools \
    --gzvcf custom_Sig_18_tumor_normal.strelka.somatic_indels.vcf.gz \
    --out custom_Sig_18_tumor_normal.strelka.somatic_indels \
    --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