#!/bin/bash
#SBATCH --job-name=AdapterRemoval-2.3.0-case
#SBATCH --partition=batch
#SBATCH --time=05:00

# conda commands
module load gcc/9.2.0 miniconda3
source $CONDA_PROFILE/conda.sh
conda activate /mnt/apps/prebuilt/AdapeterRemoval
export PATH=$CONDA_PREFIX/bin:$PATH

# Run AdapterRemoval commands
AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip