fastqc_run_parallel.pbs

#!/bin/bash

#########################################################
# 
# Platform: NCI Gadi HPC
# Description: run fastQC in parallel over all fastq in Fastq
# Usage: first, run 'bash fastqc_make_input.sh, 
# then execute this script with 'qsub fastqc_run_parallel.pbs'
# Details:
#       Run fastqc on all fastq, and unzip the fastqc dir for 
# 	text read of a subsequent step. FastQC can use some RAM
#	so its best to run this on hugemem. Inputs are sorted by size
#	so you can juggle node v walltime requests if there is a large 
# 	size discrepancy among your fastq. 
#
# Author: Cali Willet
# cali.willet@sydney.edu.au
# Date last modified: 18/12/2020
#
# If you use this script towards a publication, please acknowledge the
# Sydney Informatics Hub (or co-authorship, where appropriate).
#
# Suggested acknowledgement:
# The authors acknowledge the scientific and technical assistance 
# <or e.g. bioinformatics assistance of <PERSON>> of Sydney Informatics
# Hub and resources and services from the National Computational 
# Infrastructure (NCI), which is supported by the Australian Government
# with access facilitated by the University of Sydney.
# 
#########################################################


#PBS -P <project>
#PBS -N fqc
#PBS -l walltime=02:00:00
#PBS -l ncpus=48
#PBS -l mem=1500GB
#PBS -q hugemem
#PBS -W umask=022
#PBS -l wd
#PBS -o ./Logs/fastqc-3286.o
#PBS -e ./Logs/fastqc-3286.e
#PBS -lstorage=scratch/<project>

module load openmpi/4.0.2
module load nci-parallel/1.0.0
module load fastqc/0.11.7

set -e

SCRIPT=./Scripts/fastqc.sh
INPUTS=./Inputs/fastqc.inputs 

mkdir -p FastQC

NCPUS=1

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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