sbatch_step1.sh

#!/bin/bash
##### Job definition
# TODO: Edit email address below
#SBATCH --nodes=1					# OpenMP requires a single node
#SBATCH --ntasks=1					# Run a single serial task
#SBATCH --time=00:10:00				# Time limit hh:mm:ss
#SBATCH -e step1_error_%A_%a.log			# Standard error
#SBATCH -o step1_output_%A_%a.log			# Standard output
#SBATCH --job-name=bidssetup			# Descriptive job name
#SBATCH --partition=serial

##### load required modules

module load singularity

##### run container commands

# create samples under bids/code/bidscoiner
singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
	/scratch/psyc5171/containers/birc-bids_latest.sif \
	bidstrainer.py /data/bids


# reorganize the files
singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
	/scratch/psyc5171/containers/birc-bids_latest.sif \
	/data/bids/code/reorganize.sh IBRAIN002