submit01_trimmomatic.sh

#!/bin/bash
#PBS -S /bin/bash
#PBS -V
#PBS -l nodes=1:ppn=12
#PBS -M my@email.adr
#PBS -N trim
#PBS -j oe
# PBS -o /path/to/stderr-stdout/output

cd $PBS_O_WORKDIR

# FASTA sequences of adapters
ADAPTERS=omicsoft.fa

# Input folder
DIRIN=00_raw/

# Output folder
DIROUT=01_trimmed

mkdir -p $DIROUT

# Paired end
# k=0
# for file in `find $DIRIN -name "*.fastq.gz" -type f | sort`; do
# 	if [ $k = 0 ]
# 	then
# 		s1=$file
# 		k+=1
# 	else
# 		s2=$file
# 		k=0
# 		java -jar trimmomatic-0.33.jar PE -threads 12 -phred33 $s1 $s2 $DIROUT"/"`basename $s1 .fastq.gz`_paired.fastq.gz $DIROUT"/"`basename $s1 .fastq.gz`_unpaired.fastq.gz $DIROUT"/"`basename $s2 .fastq.gz`_paired.fastq.gz $DIROUT"/"`basename $s2 .fastq.gz`_unpaired.fastq.gz ILLUMINACLIP:$ADAPTERS:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36;
# 	fi
# done

# Single end
for file in `find $DIRIN -name "*.fastq.gz" -type f | sort`; do
	java -jar trimmomatic-0.33.jar SE -threads 12 -phred33 $file $DIROUT"/"`basename $file .fastq.gz`.fastq.gz ILLUMINACLIP:$ADAPTERS:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36;
done