.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (1029_3N0-T1-TDNA-1_23K7YCLT4_1_vs_1029_3N0-N1-BDNA-1_235YY7LT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/42776c65edd811ab37167bccb57231/.command.sh
Size: 503 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (1029_3N0-T1-TDNA-1_23K7YCLT4_1_vs_1029_3N0-N1-BDNA-1_235YY7LT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bgzip -c 1029_3N0-T1-TDNA-1_23K7YCLT4_1_vs_1029_3N0-N1-BDNA-1_235YY7LT3_1_somatic.vcf > 1029_3N0-T1-TDNA-1_23K7YCLT4_1_vs_1029_3N0-N1-BDNA-1_235YY7LT3_1_somatic.vcf.gz
tabix -p vcf 1029_3N0-T1-TDNA-1_23K7YCLT4_1_vs_1029_3N0-N1-BDNA-1_235YY7LT3_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