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

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/cd9b9ca7d8e9db86397a6927c0aacb/.command.sh
Size: 498 bytes
Task: NFCORE_SAREK:SAREK:VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools concat \
    --output custom_Sig_18_tumor_normal.snv_indel.merged.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 6 \
    custom_Sig_18_tumor_normal.snv_indel.tnseq.snv.vcf.gz custom_Sig_18_tumor_normal.snv_indel.strelka.indel.vcf.gz

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