trimming-pipeline-slurm.sb

#!/bin/bash -login
#SBATCH --time=72:00:00          
#SBATCH --ntasks=8               
#SBATCH --cpus-per-task=1        
#SBATCH --mem=50G                
#SBATCH --job-name trimming      
#SBATCH --mail-type=ALL
#SBATCH --mail-user=howead@msu.edu
#SBATCH --account shadeash-colej

#You need to figure out which version you want to run of Trimmomatic
#modify the qsub file
#First, put all your gzipped reads into a specific location and specify it below
#This requires that they are *gz and also have the standard R1/R2 unique naming schema

MY_PATH=/mnt/research/germs/sc-round2/metag-pipeline
TRIM_PATH=/mnt/home/howead/software/Trimmomatic-0.38
THREADS_TRIMMING=8
parallel="/mnt/home/howead/software/parallel-20120122/src/parallel"


cd $MY_PATH
mkdir trimmed-reads
for x in *R1_001*gz;
do
echo "java -jar $TRIM_PATH/trimmomatic-0.38.jar PE -phred33 -threads $THREADS_TRIMMING $x ${x%R1*}R2_001*fastq.gz trimmed-reads/${x%R1*}pe1 trimmed-reads/${x%R1*}se1 trimmed-reads/${x%R1*}pe2 trimmed-reads/${x%R1*}se2 ILLUMINACLIP:$TRIM_PATH/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36" >> trim.sh
done

cat trim.sh | ~/software/parallel-20180922/src/parallel 

#cd trimmed-reads
#for x in *se1; do echo "cat $x ${x%se1*}se2 > ${x%se1}se12"; done >> cat_se.sh
#cat cat_se.sh | ~/software/parallel-20180922/src/parallel --delay .2 -j 32 --joblog logs/runtask2.log --resume