nextflow.config

process {
    publishDir = {"${params.output_dir}/$sid/${task.process.replaceAll(':', '-')}"}
    scratch = true
    errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
    maxRetries = 3
    maxErrors = -1
    stageInMode = 'copy'
    stageOutMode = 'rsync'
    tag = { "$sid" }
    afterScript = 'sleep 1'
}

params {
    help = false
    input = false
    processes = false

    // ** TRACKING PARAMS ** //

    //** Global Options **//
    b0_thr = 10
    dwi_shell_tolerance = 20
    skip_dwi_preprocessing = false
    template_t1 = "/human-data/mni_152_sym_09c/t1"

    //** BET DWI Options **//
    initial_bet_f = 0.16
    final_bet_f = 0.16

    //** SYNTHSTRIP Options **//
    run_synthbet = false
    shells = "0 1500"
    shell_thr = 50
    gpu = false
    border = false
    nocsf = false
    weights = false

    //** BET ANAT Options **//
    run_bet_anat = false
    bet_anat_f = 0.16

    // EDDY and TOPUP Options
    topup_config = "b02b0.cnf"
    encoding_direction = "y"
    readout = 0.062
    topup_prefix = "topup_results"
    topup_bet_f = 0.16
    eddy_cmd = "eddy_cpu"
    use_slice_drop_correction = true

    // NORMALIZE Options
    fa_mask_threshold = 0.4

    // RESAMPLE_ANAT Options
    anat_resolution = 1
    anat_interpolation = "lin"
    mask_interpolation = "nn"

    // RESAMPLE_DWI Options
    dwi_resolution = 1
    dwi_interpolation = "lin"
    mask_dwi_interpolation = "nn"

    // EXTRACT_DTI_SHELLS Options
    dti_shells = false
    max_dti_shell_value = 1200

    // SH_FITTING_SHELL Options
    sh_fitting = false
    sh_fitting_order = 6
    sh_fitting_basis = "descoteaux07"

    // FODF Options
    fodf_shells = false
    min_fodf_shell_value = 700
    fodf_metrics_a_factor = 2.0
    max_fa_in_ventricle = 0.1
    min_md_in_ventricle = 0.003
    relative_threshold = 0.1
    basis = "descoteaux07"
    sh_order = 8

    // FRF Options
    mean_frf = false
    fa = 0.7
    min_fa = 0.5
    min_nvox = 300
    roi_radius = 20
    set_frf = true
    manual_frf = "15,4,4"

    // ** Segment Tissues Options ** //
    number_of_tissues = 3

    //** PFT Seeding and Tracking Options **//
    run_pft_tracking = true
    pft_compress_streamlines = true

    pft_seeding_mask_type = "wm"
    pft_fa_seeding_mask_thr = 0.1

    pft_algo = "prob"
    pft_nbr_seeds = 10
    pft_seeding = "npv"
    pft_step_size = 0.5
    pft_theta = 20
    pft_sfthres = 0.1
    pft_sfthres_init = 0.5
    pft_min_len = 20
    pft_max_len = 200
    pft_particles = 15
    pft_back = 2
    pft_front = 1
    pft_compress_value = 0.2
    pft_random_seed = 0

    //** Local Seeding and Tracking Options **//
    run_local_tracking = false
    local_compress_streamlines = true

    local_fa_tracking_mask_thr = 0.1
    local_tracking_mask_type = "wm"
    local_fa_seeding_mask_thr = 0.1
    local_seeding_mask_type = "wm"
    
    local_algo = "prob"
    local_nbr_seeds = 10
    local_seeding = "npv"
    local_step_size = 0.5
    local_theta = 20
    local_sfthres = 0.1
    local_sfthres_init = 0.5
    local_min_len = 20
    local_max_len = 200
    local_tracking_seed = 0
    local_compress_value = 0.2
    local_erosion = 0

    // Processes per tasks
    processes_denoise_dwi = 4
    processes_denoise_t1 = 4
    processes_bet_t1 = 4
    processes_eddy = 4
    processes_registration = 4
    processes_fodf = 4

    // ** CONNECTOMICS PARAMS ** //

    // Decompose Connectivity Options
    no_pruning = false
    no_remove_loops = false
    no_remove_outliers = false
    min_length = 20
    max_length = 200
    loop_max_angle = 330
    outlier_threshold = 0.5

    //** COMPUTE_PRIORS Options **//
    compute_priors = false
    fa_min_priors = 0.7
    fa_max_priors = 0.1
    md_min_priors = 0.002
    roi_radius_priors = 20
    multishell = false

    //** COMMIT Options **//
    run_commit = true
    use_commit2 = true
    use_both_commit = false
    commit_on_trk = false
    b_thr = 50
    nbr_dir = 500
    ball_stick = true
    para_diff = "1.7E-3"
    perp_diff = "0.51E-3"
    iso_diff = "2.0E-3"

    // Processes per tasks
    processes_commit = 8
    processes_afd_fixel = 4
    processes_connectivity = 4
    params.commit_memory_limit = '24.GB'

    // Profiles Options
    run_freesurfer = false
    run_tracking = false
    run_connectomics = false
    infant_config = false
    template_config = false
    priors = false

    // Template Options //
    references = "./references/"

    Mean_FRF_Publish_Dir = "./Results_ChildBrainFlow/Mean_FRF"
    Pop_Avg_Publish_Dir = "./Results_ChildBrainFlow/Pop_Avg"

    // ** FreeSurfer Options ** //
    recon_all = false
    recon_surf = true
    use_freesurfer_atlas = false
    use_brainnetome_atlas = false
    use_brainnetome_child_atlas = true
    use_glasser_atlas = false
    use_schaefer_100_atlas = false
    use_schaefer_200_atlas = false
    use_schaefer_400_atlas = false
    use_lausanne_1_atlas = false
    use_lausanne_2_atlas = false
    use_lausanne_3_atlas = false
    use_lausanne_4_atlas = false
    use_lausanne_5_atlas = false
    use_dilated_labels = false
    nb_threads = 4
    atlas_utils_folder = "/FS_BN_GL_SF_utils/"
    compute_FS_BN_GL_SF = false
    compute_BN_child = true
    compute_lausanne_multiscale = false
    compute_lobes = false

    // ** Output Options ** //
    output_dir = "./Results_ChildBrainFlow/"
}

if ( params.output_dir ) {
    params.Mean_FRF_Publish_Dir = "${params.output_dir}/Mean_FRF"
    params.Pop_Avg_Publish_Dir = "${params.output_dir}/Pop_Avg"
}

if(params.processes) {
    if(params.processes > Runtime.runtime.availableProcessors()) {
        throw new RuntimeException("Number of processes higher than available CPUs.")
    }
    else if(params.processes < 1) {
        throw new RuntimeException("When set, number of processes must be >= 1 " +
                                   "and smaller or equal to the number of CPUs.")
    }
    else {
        executor.$local.cpus = params.processes
    }
}

singularity.autoMounts = true

profiles {
    no_symlink {
        process{
            publishDir = [path: {"${params.output_dir}/$sid/${task.process.replaceAll(':', '-')}"}, mode: 'copy']
        }
    }

    macos {
        process.scratch="/tmp"
    }

    hcp {
        process {
            executor = 'slurm'
            errorStrategy = 'retry'
            maxRetries = 1
        }
	executor {
            pollInterval = '180 sec'
            queueGlobalStatus = true
            queueStatInterval = '3 min'
            submitRateLimit = '100/1min'
            maxForks = 1000
            queueSize = 1000
            exitReadTimeout = '600 sec'
	}
    }

    freesurfer {
        params.run_freesurfer = true
    }

    tracking {
        params.run_tracking = true
    }

    connectomics {
        params.run_connectomics = true
        
    }

    priors {
        params.priors = true
        params.run_commit = true
        params.compute_priors = true
        params.set_frf = false
        params.mean_frf = true
    }

    infant {

        params.infant_config = true
        
        //** BET DWI Options **//
        params.initial_bet_f = 0.5
        params.final_bet_f = 0.35

        //** SYNTHSTRIP Options **//
        params.run_synthbet = true

        //** NORMALIZE Options **//
        params.fa_mask_threshold = 0.10

        //** FODF Options **//
        params.max_fa_in_ventricle = 0.1
        params.min_md_in_ventricle = 0.00185

        //** FRF Options **//
        params.manual_frf = "12,5,5"

        //** LOCAL TRACKING **//
        params.run_pft_tracking = false
        params.run_local_tracking = true
        params.erosion = 6
        params.local_min_len = 15
        params.local_fa_seeding_mask_thr = 0.1

        // ** DECOMPOSE Options ** //
        min_length = 10
        outlier_threshold = 0.4

        // ** COMMIT Options ** //
        params.run_commit = true
        params.use_commit2 = true
        // params.commit_on_trk = true
        params.para_diff = "1.2E-3"
        params.iso_diff = "2.0E-3"

    }

    template {
        params.template_config = true

        //** BET ANAT Options **//
        params.bet_anat_f = 0.1

    }
}