.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES (custom_Sig_18_tumor_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/c5a968fd8e3c753c208138b7ba0cb5/.command.sh
Size: 364 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
tabix -l custom_Sig_18_tumor_normal.snv_indel.merged.vcf.gz > custom_Sig_18_tumor_normal.chromosomes.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS