#!/bin/bash
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=36
#SBATCH --mem=120Gb
#SBATCH --export=NONE
#SBATCH --mail-user=thpalma@uri.edu
#SBATCH --mail-type=END,FAIL

# Load Trimmomatic module
module load Trimmomatic/0.39-Java-11

# Check that the correct number of arguments were provided
if [ "$#" -ne 3 ]; then
    echo "Usage: $0 input_dir output_dir trimming_params"
    exit 1
fi

# Parse the input arguments
input_dir="$1"
output_dir="$2"
trimming_params="$3"

# Create output directory if it doesn't exist
mkdir -p $output_dir

# Process each input file using Trimmomatic
for file in $input_dir/*.fastq; do
    # Define output filename
    base=$(basename $file)
    output_file=$output_dir/${base%.*}_trimmed.fastq

    # Use Trimmomatic to trim the input file
    java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar SE -phred33 $file $output_file $trimming_params
done