.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (T18-D0003255)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/1bfa6f6d6fcc41357a3025689ccb9f/.command.sh
Size: 532 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (T18-D0003255)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i T18-D0003255.md.bam \
     \
    --algo HsMetricAlgo \
    --targets_list targets/prenatal-exome-v1-targets-hg38.bed \
    --baits_list baits/prenatal-exome-v1-probes-hg38.bed \
    T18-D0003255_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