run_trimmomatic.sh

#!/bin/sh

# Trim the paired reads

# Trimmomatic expects adapter sequence in current directory.
# Choices include: TruSeq3-SE.fa TruSeq3-PE.fa NexteraPE-PE.fa
# TruSeq2 was for GA II. TruSeq3 is for HiSeq, NextSeq, MiSeq.
# The TruSeq3-PE-2.fa file contains TruSeq3-PE plus more. 

# This script trims the R1 and R2 reads in tandem.
# This script assumes the read filenames follow a specific pattern.
# It finds all files that match the patterns.
# It also uses all files that have R2 in place of R1.
PATTERN="*_R1_*.fastq"
echo "WORKING ON FILES LIKE PATTERN ${PATTERN}"
echo "WORKING ON THESE FILES SPECIFICALLY:"
ls ${PATTERN}

# Optionally, this can submit each pair of files in parallel.
# This command demonstrates usage on the SGE grid at JCVI.
# This reserves 4 threads on the grid.
GRID="qsub -cwd -A DHSSDB -N trim -P 8370 -pe threaded 4"
# Here we disable the grid option.
# The next line insures this job will run local and in serial.
GRID=""
echo "GRID OPION IS: $GRID"

JPATH=/usr/local/packages/trimmomatic-0.35
APATH="adapters"
ADAPT="TruSeq3-PE-2.fa"
echo "LOOKING FOR PROGRAM JAR FILE AND ADAPTER FILE"
echo JPATH ${JPATH}
echo APATH ${APATH}
echo ADAPT ${ADAPT}
cp -v ${JPATH}/${APATH}/${ADAPT} .

ENCODING="-phred33"
ENCODING=""     # trimmomatic will determine this automatically
THREADS="-threads 4"

for FF in ${PATTERN} ;
do
    
    INFILE1=$FF
    INFILE2=`echo $INFILE1 | sed 's/_R1_/_R2_/'`
    OUTPAIR1=trim.pair.${INFILE1}
    OUTPAIR2=trim.pair.${INFILE2}
    OUTSING1=trim.sing.${INFILE1}
    OUTSING2=trim.sing.${INFILE2}

    date
    CMD="${GRID} java -jar ${JPATH}/trimmomatic-0.35.jar PE ${ENCODING} ${INFILE1} ${INFILE2} ${OUTPAIR1} ${OUTSING1} ${OUTPAIR2} ${OUTSING2} ILLUMINACLIP:${ADAPT}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ${THREADS}"
    echo $CMD
    $CMD
    echo -n $?; echo " exit status"
    date
done
echo "DONE"