.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (HCC1395_tumor_vs_HCC1395_BL;manta)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/05b1bd5e707788bddc93fce96c5365/.command.sh
Size: 390 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (HCC1395_tumor_vs_HCC1395_BL;manta)
Attempt

Content

#!/bin/bash -Ceuo pipefail
vcftools \
    --gzvcf HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.vcf.gz \
    --out HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv \
    --TsTv-by-count \
     \


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