qmtraffic_hpc

#!/bin/bash
#
# Shell script to run the QMTraffic program from inside the QMTools Docker container.
# This script mounts the required directories and call the tool inside the container.
#
# echo "ARGS=$*"

PROG=$0

export SIF=${SIF:-/contrib/singularity/shared/neuroimaging}

if [ $# -lt 2  -o "$1" = "-h" -o "$1" = "--help" ]
then
  echo "Usage: $PROG [-h] [-r REPORT_DIR] modality group_file"
  echo '  where:'
  echo '     modality   = Modality of the MRIQC group file. Must be one of: bold, T1w, or T2w.'
  echo '     group_file = Path to MRIQC group file in "inputs" subdirectory.'
  echo ''
  echo '  options:'
  echo '    -h, --help     Show this help message and exit.'
  echo '    -r REPORT_DIR, --report-dir REPORT_DIR
                           Optional name of report subdirectory in main reports directory.'
  echo ''
  echo "  example 1: $PROG bold inputs/sample_bold.tsv"
  echo "  example 2: $PROG bold inputs/sample_bold.tsv -r sample_traffic_report"
  exit 1
fi

apptainer exec --pwd / --bind ${PWD}/inputs:/inputs:ro --bind ${PWD}/reports:/reports ${SIF}/qmtools_latest.sif qmtraffic -v $@