fastqc.sh

#!/bin/bash

##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: this script is run by fastqc_run_parallel.pbs
# Version: 2.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
#
# 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 support provided by the Sydney Informatics Hub,
# a Core Research Facility of the University of Sydney. This research/project
# was undertaken with the assistance of resources and services from the National
# Computational Infrastructure (NCI), which is supported by the Australian
# Government, and the Australian BioCommons which is enabled by NCRIS via
# Bioplatforms Australia funding.
#
##########################################################################

fastq=`echo $1 | cut -d ',' -f 1`
out=`echo $1 | cut -d ',' -f 2`
logfile=`echo $1 | cut -d ',' -f 3`

echo "$(date): Running fastQC. Fastq:${fastq}, Output:${out}, Log file: ${logfile}, NCPUS:${NCPUS}" >> ${logfile} 2>&1

fastqc -t ${NCPUS} --extract -o ${out} ${fastq} >> ${logfile} 2>&1