gatk4_getpileupsummaries_missing_run_parallel.pbs

#!/bin/bash

#########################################################
#
# Platform: NCI Gadi HPC
# Usage: qsub gatk4_getpileupsummaries_missing_run_parallel.pbs
# Version: 1.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Somatic-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.
#
#########################################################

# Run GATK4 GetPileupSummaries
# 1 task = 1 bam
# 28Gb mem per task, ~ 25min walltime

#PBS -P 
#PBS -N getpileupsummaries
#PBS -l walltime=15:00:00,ncpus=48,mem=1500GB,wd
#PBS -q hugemem
#PBS -W umask=022
#PBS -l storage=XXX
#PBS -o ./Logs/gatk4_getpileupsummaries/getpileupsummaries_missing.o
#PBS -e ./Logs/gatk4_getpileupsummaries/getpileupsummaries_missing.e

set -e

module load openmpi/4.1.0
module load nci-parallel/1.0.0a
module load gatk/4.2.1.0

# SCRIPT
SCRIPT=./gatk4_getpileupsummaries.sh
INPUTS=./Inputs/gatk4_getpileupsummaries_missing.inputs

NCPUS=2 # CPUs per task

echo "$(date): GATK 4 GetPileupSummaries for tumour normal pairs"


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# Do not edit below this line
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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