.command.sh - Workdir - DAQ:MARKDUPLICATES_SENTIEON (1029_BICJ-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/7e9a8a006beae9b40e521eef1ddc92/.command.sh
Size: 634 bytes
Task: DAQ:MARKDUPLICATES_SENTIEON (1029_BICJ-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver -t 31 -i 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector  --fun score_info 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.score

sentieon driver -t 31 -i 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup  --score_info 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1029_BICJ-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