nextflow.config

nextflow.enable.dsl=2

manifest {
    name = "Kumar Lab Mouse Tracking Pipelines"
    homePage = "https://github.com/KumarLabJax/mouse-tracking-runtime"
    mainScript = "main.nf"
    defaultBranch = 'main'
    nextflowVersion = "!>=22.04.3"
    version = "0.2.5"
    contributors = [
        [name: 'Brian Geuther'],
        [name: 'Alexander Berger-Liedtka']
    ]
}

params {
    /*
     * Parameters:
     * - input_batch: file containing a list of input video files
     * - pipeline: processing pipeline, single-mouse or multi-mouse
     * - profile: processing profile, sumner2 or development
     * - batch_timestamp: timestamp when the batch initiated
     * - batch_name: name of the batch
     * - location: location of the data, local or dropbox
     * - path_depth: depth of the path to preserve in the output
     * - pubdir: directory to publish the results (defaults in profiles)
     */
    input_batch = null
    ignore_invalid_inputs = false
    profile = 'sumner2'
    corner_frame = 100
    batch_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
    batch_name = "batch_${batch_timestamp}"
    location = 'local'
    path_depth = 2

    /* Image Versions */
    image_version = '0.2.5'
    jabs_postprocess_version = '0.5.4'
    jabs_behavior_version = '0.36.1'

    /*
     * Parameters for the single mouse pipeline
     * - align_videos: align videos to a common start time
     * - clip_duration: duration of the video clips in frames
     */
    align_videos = true
    clip_duration = 108000

    /*
     * Parameters for the static object correction pipeline
     * - sleap_file: path to the sleap file containing manual annotations
     */
    sleap_file = null

    /*
     * Parameters for the multi mouse pipeline
     * - num_mice: number of mice in the video
     */
    num_mice = 3

    git_hash = 'git rev-parse HEAD'.execute().text.trim() ?: 'unknown'
}

profiles {
    development  { includeConfig "nextflow/configs/profiles/development.config" }
    sumner2      { includeConfig "nextflow/configs/profiles/sumner2.config" }
}

env {
    MOUSE_TRACKING_MODEL_DIRECTORY = "${params.model_dir}"
}