.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2 (PatientC_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/e31eefb1eb10d471578f0aa5e70c57/.command.sh
Size: 558 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2 (PatientC_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
echo | gzip > PatientC_normal.tnseq_tumor_only.vcf.gz
touch PatientC_normal.tnseq_tumor_only.vcf.gz.tbi
touch PatientC_normal.tnseq_tumor_only.vcf.gz.stats
touch PatientC_normal.tnseq_tumor_only.orientation_data.tsv
touch PatientC_normal.tnseq_tumor_only.{contamination_data.tsv,segments}

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" )
END_VERSIONS