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split_fastq_make_input.sh
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split_fastq_make_input.sh
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#!/bin/bash
##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: bash split_fastq_make_input.sh <config prefix>
# 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.
#
##########################################################################
cohort=../$1
inputs=./Inputs/split_fastq.inputs
rm -f $inputs
awk 'NR>1' ${cohort}.config | while read sample
do
sample=`echo $sample | cut -f 1 -d ' '`
#echo $sample #use this to check $sample is correctly capturing your sampleID
# find fastq pairs for each $sample. Check regex matches your samples
fqpairs=$(find ../Fastq/ -name *${sample}*.f*q.gz | sed 's/.R1.*\|.R2.*\|_R1.*\|_R2.*\|_R1_*\|_R2_*//' | sort | uniq )
#echo $fqpairs #use this to check $fqpairs is capturing your fqs
# print fq pair info to input file
printf '%s\n' $fqpairs >> $inputs
done
tasks=`wc -l < ${inputs}`
printf "Number of fastq pairs to split: ${tasks}\n"
printf "\nIf you changed the \$fqpair regex in this script please confirm it matches \$fq1 and \$fq2 regex in the split_fastq.sh script before running split_fastq_run_parallel.pbs!!!\n"
printf "You will also need to change the regex in the split_fastq_check_fastq_input scripts and the align scripts in order to run them successfully"