.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (T21-D0003376)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/d5c5af50d4a9c55843c4276d21a3e2/.command.sh
Size: 532 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (T21-D0003376)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i T21-D0003376.md.bam \
     \
    --algo HsMetricAlgo \
    --targets_list targets/prenatal-exome-v1-targets-hg38.bed \
    --baits_list baits/prenatal-exome-v1-probes-hg38.bed \
    T21-D0003376_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