Updated SBATCH script for MRIQC protocol manuscript

docs/source/resources/mriqc.sbatch

@@ -0,0 +1,61 @@
+#!/bin/bash
+#NOTE: These should work with Slurm HPC systems, 
+ # but these specific parameters  have only been tested on 
+ # Stanford's Sherlock. Some parameters may need to be 
+ # adjusted for other HPCs, specifically --partition.
+#SBATCH --job-name mriqc
+#SBATCH --partition normal #TODO: update for your HPC
+#NOTE: The --array parameter allows multiple jobs to be launched at once, 
+ # and is generally recommended to efficiently run several hundred jobs 
+ # at once.
+# TODO: adjust the range for your dataset; 1-n%j where n is the number of 
+ # participants and j is the maximum number of concurrent jobs you'd like 
+ # to run. 
+#SBATCH --array=1-216%50
+#SBATCH --time=1:00:00 #NOTE: likely longer than generally needed 
+#SBATCH --ntasks 1
+#SBATCH --cpus-per-task=16
+#SBATCH --mem-per-cpu=4G
+# Outputs ----------------------------------
+#SBATCH --output log/%x-%A-%a.out
+#SBATCH --error log/%x-%A-%a.err
+#SBATCH --mail-user=%[email protected] #TODO: update for your email domain
+#SBATCH --mail-type=ALL
+
+# ------------------------------------------
+
+STUDY="/scratch/users/mphagen/mriqc-protocol" #TODO: replace with your path
+
+
+MRIQC_VERSION="24.0.2" #TODO: update if using a different version
+BIDS_DIR="${STUDY}/ds002785"  # TODO: replace with path to your dataset
+OUTPUT_DIR="${BIDS_DIR}/derivatives/mriqc-${MRIQC_VERSION}"
+
+APPTAINER_CMD="apptainer run -e mriqc_${MRIQC_VERSION}.sif"
+
+# Offset subject index by 1 because of header in participants.tsv   
+subject_idx=$(( ${SLURM_ARRAY_TASK_ID} + 1 ))
+
+##NOTE: The first clause in this line selects a row in participants.tsv 
+ # using the system generated array index variable SLURM_ARRAY_TASK_ID. 
+ # This is piped to grep to isolate the subject id. The regex should 
+ # work for most subject naming conventions, but may need to be modified.
+
+subject=$( sed -n ${subject_idx}p ${BIDS_DIR}/participants.tsv \
+ | grep -oP "sub-[A-Za-z0-9_]*" ) 
+
+echo Subject $subject
+
+cmd="${APPTAINER_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant \
+     --participant-label $subject \
+     -w $PWD/work/ \
+     --omp-nthreads 10 --nprocs 12"  # For nodes with at least 32GB RAM
+
+echo Running task ${SLURM_ARRAY_TASK_ID}
+echo Commandline: $cmd
+eval $cmd
+exitcode=$?
+echo "sub-$subject   ${SLURM_ARRAY_TASK_ID}    $exitcode" \
+      >> ${SLURM_ARRAY_JOB_ID}.tsv
+echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode
+exit $exitcode