.command.sh - Workdir - DAQ:MARKDUPLICATES_SENTIEON (HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/.command.sh
Size: 502 bytes
Task: DAQ:MARKDUPLICATES_SENTIEON (HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector  --fun score_info HCC1395_BL.md.score

sentieon driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup  --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.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