#!/bin/bash

stepsize=$1; shift
subjs=($@)

#SBATCH --nodes=1
#SBATCH --tasks-per-node=16
#SBATCH --export=None

source /sw/batch/init.sh

export LD_LIBRARY_PATH="/sw/compiler/gcc-8.4.0/lib64/:$LD_LIBRARY_PATH"
module unload singularity
module switch singularity/3.5.2-overlayfix

proj_dir=/work/fatx405/projects/2104_dwiproc_hchs
source $proj_dir/.projectrc

####################
# Application of QSIprep for DWI preprocessing and connectome reconstruction
# QSIprep version 0.13.0RC2
####################

stepsize=${stepsize-1} #if stepsize is empty stepsize=1
subjs_start_idx=${SLURM_ARRAY_TASK_ID-0} #if SLURM_ARRAY_TASK_ID is empty subjs_start_idx=0
subjs=(${subjs[@]-$(ls $bids_dir/sub* -d -1)}) #if subjs empty subjs = subjects in $bids_dir
subjs_subarr=$(basename -a ${subjs[@]:$subjs_start_idx:$stepsize}) #array slicing + stripping of path

echo $stepsize
echo $subjs_start_idx
echo subjs: ${subjs[@]}
echo subjects_subarr: ${subjs_subarr[@]}

echo $(hostname)
echo $(singularity --version)

echo $PATH

unset PYTHONPATH
PATH=$(echo "$PATH" | sed -e 's/:\/work\/fatx405\/miniconda3\/bin$//')

singularity run --cleanenv --no-home --userns -B /work/fatx405/projects/2104_dwiproc_hchs/02_env:/mnt \
    -B /work/fatx405/projects/2104_dwiproc_hchs/00_data/raw_bids:/sngl/data \
    -B /work/fatx405/projects/2104_dwiproc_hchs/00_data/derivatives:/sngl/out \
    -B /work/fatx405/projects/2104_dwiproc_hchs/00_data/derivatives/qsiprep:/sngl/qsiprep-output \
    -B /work/fatx405/projects/2104_dwiproc_hchs/00_data/intermediate:/sngl/scratch \
    -B $env_dir:/sngl/env \
    /work/fatx405/projects/2104_dwiproc_hchs/02_env/qsiprep-0.13.0RC2 \
    /sngl/data /sngl/qsiprep-output participant \
    -w /sngl/scratch/ \
    --participant-label ${subjs_subarr[@]} \
    --recon_input /sngl/out/qsiprep \
    --recon_spec mrtrix_singleshell_ss3t \
    --fs-license-file /sngl/env/freesurfer_license.txt \
    --output-resolution 1.3 \
    --output-space T1w \
    --use-syn-sdc \
    -v