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

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/2b6de87f88c0901e1bbe8a58050d07/.command.sh
Size: 392 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bgzip -c HCC1395_tumor_vs_HCC1395_BL_somatic.vcf > HCC1395_tumor_vs_HCC1395_BL_somatic.vcf.gz
tabix -p vcf HCC1395_tumor_vs_HCC1395_BL_somatic.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY":
    htslib: $(tabix --version | head -1 | sed 's/tabix (htslib) //')
END_VERSIONS