File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/0e545657ffe3fbe8db5b3ae4c0be46/.command.sh
Size
509 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY (1029_4EU-T1-TDNA-1_A23MHKVLT4_1_vs_1029_4EU-N1-BDNA-1_A23KFG7LT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
bgzip -c 1029_4EU-T1-TDNA-1_A23MHKVLT4_1_vs_1029_4EU-N1-BDNA-1_A23KFG7LT4_1_somatic.vcf > 1029_4EU-T1-TDNA-1_A23MHKVLT4_1_vs_1029_4EU-N1-BDNA-1_A23KFG7LT4_1_somatic.vcf.gz
tabix -p vcf 1029_4EU-T1-TDNA-1_A23MHKVLT4_1_vs_1029_4EU-N1-BDNA-1_A23KFG7LT4_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