sbatch_mriqc.sh

#!/bin/bash

##### Job definition
# Add your SLURM options here
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jason.crutcher@uconn.edu
#SBATCH --nodes=1                                       # OpenMP requires a single node
#SBATCH --ntasks=1                                      # Run a single serial task
#SBATCH --time=01:30:00		                        # Time limit hh:mm:ss
#SBATCH -e mriqc_error_%A_%a.log                        # Standard error
#SBATCH -o mriqc_output_%A_%a.log                       # Standard output
#SBATCH --job-name=mriqc		                # Descriptive job name
#SBATCH --partition=serial
#SBATCH --mem=8gb

# load modules

module load singularity

# commands needed to run mriqc
singularity run --cleanenv \
	--bind /scratch/jac18015/hw3/mbdata/bids:/data \
	--bind /scratch/jac18015/hw3/mriqc:/out \
	/scratch/psyc5171/containers/mriqc_latest.sif \
	/data /out participant \
	--nprocs 3