.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/d2a3588977fba6d30bb3a4ea5188af/.command.sh
Size: 348 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
tabix -l HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz > HCC1395_tumor_vs_HCC1395_BL.chromosomes.txt

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