nextflow.config

process {
    publishDir = {"./results_bst/$sid/$task.process"}
    scratch = true
    stageInMode = 'copy'
    stageOutMode = 'rsync'
    tag = { "$sid" }
    afterScript = 'sleep 1'
}

params {
    help=false
    input=false
    atlas_anat=false
    atlas_directory=false
    use_atlas_roi_seeding=false

    use_orientational_priors=true
    use_bs_tracking_mask=false
    use_bs_endpoints_include=false
    bs_endpoints_mask_dilation=3
    use_tracking_mask_as_seeding=true
    bs_tracking_mask_dilation=3

    local_tracking=true
    pft_tracking=false

    seeding="npv"
    nbr_seeds=1
    algo="prob"
    sh_basis="descoteaux07"
    min_length=20
    max_length=200
    compress_error_tolerance=0.2
    tracking_seed=0

    // recobundles segmentation
    recobundles=true
    wb_clustering_thr=6
    model_clustering_thr=4
    prunning_thr=12
    outlier_alpha=0.6

    register_processes=4
}

singularity.autoMounts = true

profiles {
    fully_reproducible {
        params.register_processes=1
    }

    macos {
            process.scratch="/tmp"
    }
}