rnaseq_job_template.sub

#!/bin/bash -l
#SBATCH --mail-user=[ENTER EMAIL ADDRESS]	 # Notifications about job run
#SBATCH --mail-type=ALL                      # Email notifications on start, end, abort and cancel job status (DO NOT CHANGE)
#SBATCH --nodes=1                            # 1 node requested (DO NOT CHANGE)
#SBATCH --ntasks=20                          # 20 CPUs requested (DO NOT CHANGE)
#SBATCH -p fast.q                            # Using fast.q queue (DO NOT CHANGE)
#SBATCH --time=0-01:00:00                    # 1 hour wall time limit for job, after an hour the job will be automatically killed
#SBATCH --output=rnaseq_preprocess.stdout    # Error message ill be saved to this file (DO NOT CHANGE)
#SBATCH --job-name=[ENTER_JOB_NAME]          # Name of this job run, can be changed as per your convenience (NO_SPACES_PERMITTED)
#SBATCH --export=ALL						 # Environment variables propogated to job environment

# Load anaconda3 module
module load anaconda3

# Load RNAseq environment
source activate RNA-seq

# Command to run preprocessing and differential gene expression
INPUTFOLDER=[INSERT FULL PATH TO INPUT DATA FOLDER]

# Command to find the pipeline.sh file
scriptfile=$(find ~ -type f -name "pipeline.sh" -exec realpath {} \;)

# Command to execute the scriptfile
bash "${scriptfile}" "${INPUTFOLDER}" > "${INPUTFOLDER}"/preprocess.log