#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/2021-09-08_rings/
cd $WORK_DIR;
#mkdir cutadapt;
# Declare a string array with type
declare -a files=("G1_S5" "G2_S6" "G3_S7")

for file in for file in "${files[@]}"
do
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o $WORK_DIR/cutadapt/cutIL_${file}_L001_R1_001.fastq.gz -p $WORK_DIR/cutadapt/cutIL_${file}_L001_R2_001.fastq.gz $WORK_DIR/raw/${file}_L001_R1_001.fastq.gz $WORK_DIR/raw/${file}_L001_R2_001.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}_L001_R1_001.fastq.gz -p $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${file}_L001_R2_001.fastq.gz --overlap 20 $WORK_DIR/cutadapt/cutIL_${file}_L001_R1_001.fastq.gz $WORK_DIR/cutadapt/cutIL_${file}_L001_R2_001.fastq.gz;
done
