From 2e6d03b0b7c591b8a83d4a962e207110ccc0e19c Mon Sep 17 00:00:00 2001
From: McKenzie Paige Hagen <mphagen@uw.edu>
Date: Mon, 14 Oct 2024 20:08:42 -0700
Subject: [PATCH] switch singularity to apptainer

---
 docs/source/resources/mriqc.sbatch | 34 +++++++++++++++---------------
 1 file changed, 17 insertions(+), 17 deletions(-)
 mode change 100644 => 100755 docs/source/resources/mriqc.sbatch

diff --git a/docs/source/resources/mriqc.sbatch b/docs/source/resources/mriqc.sbatch
old mode 100644
new mode 100755
index 9327b00d..2a6e86b7
--- a/docs/source/resources/mriqc.sbatch
+++ b/docs/source/resources/mriqc.sbatch
@@ -1,21 +1,16 @@
 #!/bin/bash
-
 #NOTE: These should work with Slurm HPC systems, 
- # but these specific paramters  have only been tested on 
+ # 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
@@ -26,31 +21,36 @@
 #SBATCH --error log/%x-%A-%a.err
 #SBATCH --mail-user=%u@stanford.edu #TODO: update for your email domain
 #SBATCH --mail-type=ALL
+
 # ------------------------------------------
 
-unset PYTHONPATH
+STUDY="/scratch/users/mphagen/mriqc-protocol" #TODO: replace with your path
 
-MRIQC_VERSION="24.0.0" #TODO: update if using a different version
-BIDS_DIR="ds002785" #TODO: replace with path to your dataset
+
+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}"
 
-SINGULARITY_CMD="singularity run -e mriqc-${MRIQC_VERSION}.simg"
+APPTAINER_CMD="apptainer run -e mriqc_${MRIQC_VERSION}.sif"
 
-#NOTE: The first clause in this line selects a row in participants.tsv 
+# 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 ${SLURM_ARRAY_TASK_ID}p ${BIDS_DIR}/participants.tsv \
+ # work for most subject naming conventions, but may need to be modified.
+ 
+subject=$( sed -n ${subject_idx}p ${BIDS_DIR}/participants.tsv \
  | grep -oP "sub-[A-Za-z0-9_]*" ) 
 
 echo Subject $subject
 
-cmd="${SINGULARITY_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant \
+cmd="${APPTAINER_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant \
      --participant-label $subject \
      -w $PWD/work/ \
-     --omp-nthreads 8 --mem 10 \
-     --verbose-reports"
+     --omp-nthreads 10 --nprocs 12 \
+     --verbose-reports" 
 
 echo Running task ${SLURM_ARRAY_TASK_ID}
 echo Commandline: $cmd