gatk4_genomicsdbimport_missing_run_parallel.pbs

#!/bin/bash

#########################################################
# 
# Platform: NCI Gadi HPC 
# Usage: 
# Version: 2.0 
# 
# For more details see: https://github.com/Sydney-Informatics-Hub/Germline-ShortV 
# 
# If you use this script towards a publication, support us by citing: 
# 
# Suggest citation: 
# Sydney Informatics Hub, Core Research Facilities, University of Sydney, 
# 2021, The Sydney Informatics Hub Bioinformatics Repository, <date accessed>, 
# https://github.com/Sydney-Informatics-Hub/Germline-ShortV 
# 
# Please acknowledge the Sydney Informatics Hub and the facilities: 
# 
# Suggested acknowledgement: 
# The authors acknowledge the technical assistance provided by the Sydney 
# Informatics Hub, a Core Research Facility of the University of Sydney 
# and the Australian BioCommons which is enabled by NCRIS via Bioplatforms 
# Australia. The authors acknowledge the use of the National Computational 
# Infrastructure (NCI) supported by the Australian Government. 
# 
#########################################################

#PBS -P <project>
#PBS -N genomicsdbimport_missing
#PBS -l walltime=00:00:00,ncpus=,mem=GB,wd
#PBS -q hugemem
#PBS -W umask=022
#PBS -l storage=
#PBS -o ./Logs/gatk4_genomicsdbimport_missing.o
#PBS -e ./Logs/gatk4_genomicsdbimport_missing.e

set -e

# NCPUs = CPUs per task
NCPUS=12

INPUTS=./Inputs/gatk4_genomicsdbimport_missing.inputs

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# Do not edit below this line
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module load openmpi/4.1.0
module load nci-parallel/1.0.0a
module load gatk/4.1.8.1

# SCRIPT
SCRIPT=./gatk4_genomicsdbimport_missing.sh

echo "$(date) : GATK 4 Consolidate VCFs across samples with GenomicsDBImport."

if [[ $PBS_QUEUE =~ bw-exec ]]; then CPN=28; else CPN=48; fi
M=$(( CPN / NCPUS )) #tasks per node

sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file

mpirun --np $((M * PBS_NCPUS / CPN)) \
        --map-by node:PE=${NCPUS} \
        nci-parallel \
        --verbose \
        --input-file ${PBS_JOBFS}/input-file