.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (1029_1O-T1-TDNA-1_B23VCL7LT4_1_vs_1029_1O-N1-BDNA-1_B23MHTGLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/fc080253e18a98f92fd77547562c7c/.command.sh
Size: 503 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (1029_1O-T1-TDNA-1_B23VCL7LT4_1_vs_1029_1O-N1-BDNA-1_B23MHTGLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bgzip -c 1029_1O-T1-TDNA-1_B23VCL7LT4_1_vs_1029_1O-N1-BDNA-1_B23MHTGLT4_1_somatic.vcf > 1029_1O-T1-TDNA-1_B23VCL7LT4_1_vs_1029_1O-N1-BDNA-1_B23MHTGLT4_1_somatic.vcf.gz
tabix -p vcf 1029_1O-T1-TDNA-1_B23VCL7LT4_1_vs_1029_1O-N1-BDNA-1_B23MHTGLT4_1_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