gatk4_hc_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 gatk4_hc_missing
#PBS -l walltime=00:00:00,ncpus=,mem=GB,wd
#PBS -q normal
#PBS -W umask=022
#PBS -l storage=scratch/<project>
#PBS -o ./Logs/gatk4_hc_missing.o
#PBS -e ./Logs/gatk4_hc_missing.e

set -e

INPUTS=./Inputs/gatk4_hc_missing.inputs

# NCPUS = CPUs per task
NCPUS=1

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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_hc.sh

M=$(( PBS_NCI_NCPUS_PER_NODE / NCPUS )) #tasks per node

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

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