#!/bin/bash

# Set your SCC project
#$ -P tutorial

# Specify hard time limit for the job.
#   The job will be aborted if it runs longer than this time.
#   The default time is 12 hours
#$ -l h_rt=12:00:00

# Send an email when the job finishes or if it is aborted (by default no email is sent).
#$ -m ea

# Give job a name
#$ -N mriqc_example

# Combine output and error files into a single file
#$ -j y

#$ -pe omp 4
#$ -l mem_per_core=4G

# Keep track of information related to the current job
echo "=========================================================="
echo "Start date : $(date)"
echo "Job name : $JOB_NAME"
echo "Job ID : $JOB_ID  $SGE_TASK_ID"
echo "=========================================================="

# now that our dataset is BIDS valid, lets run MRIQC!
# running MRIQC is pretty easy!

# load the mriqc module
module load mriqc

# specify where on the SCC your BIDS formatted data lives
BIDS_DIR='/projectnb/tutorial/tuta0/bids'

# specify where on the SCC you want the output reports to be written
OUTPUT_DIR='/projectnb/tutorial/tuta0/bids/derivatives/mriqc'

# specify where on the SCC you want temporary files to be written. Defaulting here to your job's temporary directory
WORK_DIR=$TMP

# request computational resources
NCORES=$NSLOTS
NTHREADS=$NSLOTS
MEM=16

# run MRIQC
mriqc $BIDS_DIR $OUTPUT_DIR participant -w $WORK_DIR --no-sub --nprocs $NCORES --omp-nthreads $NTHREADS --mem $MEM