#PBS -q bl2x220g7q
#PBS -l select=1:ncpus=5:mem=10g
#PBS -l walltime=01:00:00
#PBS -l cput=01:00:00

source ~/programms/ame/bin/activate
WORK_DIR=~/loxP_project/2022-05-23_rings/
cd $WORK_DIR;
mkdir cutadapt;
# Declare a string array with type
declare -a files=("VIR1_1" "VIR1_2" "VIR1_3" "VIR1_4" "VIR2_1" "VIR2_2" "VIR2_3" "VIR2_4")

for file in "${files[@]}"
do
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o $WORK_DIR/cutadapt/cutIL_${file}_R1.fq.gz -p $WORK_DIR/cutadapt/cutIL_${file}_R2.fq.gz $WORK_DIR/raw/${file}/${file}_R1.fastq.gz $WORK_DIR/raw/${file}/${file}_R2.fastq.gz -m 8;
wait;
cutadapt -g ada1=AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -g ada2=ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -G ada1=AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -G ada2=ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -o $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${file}_R1.fq.gz -p $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${file}_R2.fq.gz $WORK_DIR/cutadapt/cutIL_${file}_R1.fq.gz $WORK_DIR/cutadapt/cutIL_${file}_R2.fq.gz --overlap 20;
done
