1.5.cat.files

#!/bin/bash

source globals

DIR=$0.dir
mkdir -p $DIR

input_arg=""
sample_arg=""
first=1

for sample in $SAMPLES
do
	paired_fq=1.join_paired_ends.dir/$sample.min_overlap_$J/fastqjoin.join.fastq
	if [ $first -eq 1 ]
	then
		input_arg="$paired_fq"
		first=0
	else
		input_arg="$input_arg $paired_fq"
	fi
done

echo cating files 

mkdir 1.5.quality.filtering
cat $input_arg > 1.5.quality.filtering/cat.all.joined.bacteria.seqs.fastq