.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (SH032_HG513)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/9a0e9379e8a6e4f2be6c971ffe6ccb/.command.sh
Size: 530 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (SH032_HG513)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i SH032_HG513.md.bam \
     \
    --algo HsMetricAlgo \
    --targets_list targets/prenatal-exome-v1-targets-hg38.bed \
    --baits_list baits/prenatal-exome-v1-probes-hg38.bed \
    SH032_HG513_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics

cat <<-END_VERSIONS > versions.yml
"DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS