bqsr_gather_serial.pbs

#!/bin/bash

##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: qsub bqsr_gather_serial.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.
#
##########################################################################

#PBS -P 
#PBS -N bqsr_gather
#PBS -l walltime=00:00:00
#PBS -l ncpus=
#PBS -l mem=GB
#PBS -q express
#PBS -W umask=022
#PBS -l wd
#PBS -o ./Logs/bqsr_gather_serial.o
#PBS -e ./Logs/bqsr_gather_serial.e
#PBS -lstorage=

module load gatk/4.1.8.1

set -e

while read SAMPLE
do
        tables=$(find ../BQSR_tables -name "${SAMPLE}.*.recal_data.table")
        tables=($tables)
        tables_list=''

        for file in ${tables[@]}
        do
                tables_list+=" -I $file"
        done

        gatk GatherBQSRReports \
                $tables_list \
                -O ../BQSR_tables/${SAMPLE}.recal_data.table
done < ./Inputs/bqsr_gather.inputs*