# This is an example config yaml file for:
#   BIDS App:         fMRIPrep ("fmriprep")
#   BIDS App version: 25-0-0
#   Task:             `--anat-only` mode
#   Which system:     SGE or Slurm

# WARNING!!!
#   This is only an example, which may not necessarily fit your purpose,
#   or be an optimized solution for your case,
#   or be compatible to the BIDS App version you're using.
#   Therefore, please change and tailor it for your case before use it!!!

# Arguments in `singularity run`:
bids_app_args:
    $SUBJECT_SELECTION_FLAG: "--participant-label"
    -w: "$BABS_TMPDIR"
    --stop-on-first-crash: ""
    --fs-license-file: "/cbica/software/external/freesurfer/centos7/5.3.0/license.txt"
    --output-spaces: "MNI152NLin6Asym:res-1"
    --force: "bbr"
    --skip-bids-validation: ""
    -vv: ""
    --anat-only: "" #runs only anatomical workflow of fmriprep
    --cifti-output: "91k"
    --n_cpus: "2"
    --mem-mb: "12000"

# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
#   As fMRIPrep will use BIDS output layout, we need to ask BABS to create a folder 'fmriprep_anat' to wrap all derivatives:
all_results_in_one_zip: true
zip_foldernames:
    fmriprep_anat: "25-0-0" # folder 'fmriprep_anat' will be zipped into 'sub-xx_(ses-yy_)fmriprep_anat-25-0-0.zip'
# Note: The generated data can also be used to provide FreeSurfer derivatives as input dataset when running fMRIPrep on fMRI data,
#   i.e., for use case: fMRIPrep with FreeSurfer results ingressed.
#   For that case, when using `babs init`, for `--datasets`, please call this FreeSurfer derivatives dataset 'fmriprep_anat'.

# Arguments that are passed directly to singularity/apptainer:
singularity_args:
    - --containall
    - --writable-tmpfs

# How much cluster resources it needs:
cluster_resources:
    interpreting_shell: "/bin/bash"
    hard_runtime_limit: "24:00:00"
    temporary_disk_space: 200G
    customized_text: |
        #SBATCH -p all
        #SBATCH --nodes=1
        #SBATCH --ntasks=1
        #SBATCH --cpus-per-task=2
        #SBATCH --mem=12G
        #SBATCH --propagate=NONE

# Necessary commands to be run first:
script_preamble: |
    eval "$(micromamba shell hook --shell bash)"
    micromamba activate babs

# Where to run the jobs:
job_compute_space: "${TMPDIR}"

# Below is to filter out subjects (or sessions). Only those with required files will be kept.
required_files:
    $INPUT_DATASET_#1:
        - "anat/*_T1w.nii*"

# Alert messages that might be found in log files of failed jobs:
#   These messages may be helpful for debugging errors in failed jobs.
alert_log_messages:
    stdout:
        - "Excessive topologic defect encountered"
        - "Cannot allocate memory"
        - "mris_curvature_stats: Could not open file"
        - "Numerical result out of range"
        - "fMRIPrep failed"