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bqsr_gather_serial.pbs
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bqsr_gather_serial.pbs
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#!/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*