trim-and-filter.sh

#!/bin/sh
module load trimmomatic

cd /scratch/at120/gabby-laura-stats/

# for i in $(ls *fastq | perl -pe 's/\.fastq//g'); do mv $i.fastq $(echo $i | perl -pe 's/^C.+l0(\d)n0(\d)_(.+)\.3.+/$3_l$1.r$2.fastq/g'); done

# for i in $( ls *fastq | perl -pe 's/\.r\d\.fastq//g' | sort | uniq); do sbatch --export=fastq=$i trimmomatic.sh ; done
java -jar /share/apps/trimmomatic/0.36/trimmomatic-0.36.jar PE -threads 12 $fastq.r1.fastq $fastq.r2.fastq -baseout $fastq.fastq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36