.command.sh - Workdir - DAQ:MARKDUPLICATES_SENTIEON (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/.command.sh
Size: 628 bytes
Task: DAQ:MARKDUPLICATES_SENTIEON (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver -t 31 -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector  --fun score_info 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.score

sentieon driver -t 31 -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup  --score_info 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.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