.command.sh - Workdir - DAQ:MARKDUPLICATES_SENTIEON (13929215-cfDNA)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/9928b415a25e9b143a567745a14137/.command.sh
Size: 526 bytes
Task: DAQ:MARKDUPLICATES_SENTIEON (13929215-cfDNA)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver -t 31 -i 13929215-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector  --fun score_info 13929215-cfDNA.md.score

sentieon driver -t 31 -i 13929215-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo Dedup  --score_info 13929215-cfDNA.md.score --metrics 13929215-cfDNA.md.metrics 13929215-cfDNA.md.bam

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