.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_BGZIP_TABIX (custom_Sig_18_tumor_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/9ab856bfb30f20912b4b5ea847d7dd/.command.sh
Size: 387 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_BGZIP_TABIX (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bgzip -c custom_Sig_18_tumor_normal_somatic.vcf > custom_Sig_18_tumor_normal_somatic.vcf.gz
tabix -p vcf custom_Sig_18_tumor_normal_somatic.vcf.gz

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