First draft of classifier generation pipeline

nextflow/bootstrap/classifier_source.config

@@ -0,0 +1,103 @@
+// Example configuration for the classifier bootstrap pipeline.
+// Update the paths and classifiers to match your environment before running.
+
+params {
+    // Root directory where classifier artifacts will be written.
+    classifier_base_path = "/projects/kumar-lab/data/jabs/classifiers"
+
+    // Directory containing source JABS project folders referenced below.
+    classifier_project_folders = "/projects/kumar-lab/data/jabs/projects"
+
+    // Version label for this bootstrap build.
+    jabs_version = "v0.37.0"
+
+    // Map of behaviors to their source projects and metadata.
+    single_mouse_classifiers = [
+        // "grooming": [
+        //     "project_folder_name": "grooming",
+        //     "stitch_value": 10*30,
+        //     "filter_value": 3*30,
+        // ],
+        "scratch": [
+            "project_folder_name": "jabs-paper",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        // "Leg_splaying": [  // Currently can't be exported successfully
+        //     "project_folder_name": "ptz",
+        //     "stitch_value": 5,
+        //     "filter_value": 5,
+        // ],
+        "Side seizure": [
+            "project_folder_name": "ptz",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Tail jerk": [
+            "project_folder_name": "ptz",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Wild jumping": [
+            "project_folder_name": "ptz",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Escape": [
+            "project_folder_name": "jabs-vivek",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Rearing (supported)": [
+            "project_folder_name": "jabs-vivek",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Rearing (unsupported)": [
+            "project_folder_name": "jabs-vivek",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Turn left": [
+            "project_folder_name": "jabs-vivek",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+        "Turn right": [
+            "project_folder_name": "jabs-vivek",
+            "stitch_value": 5,
+            "filter_value": 5,
+        ],
+    ]
+}
+
+apptainer {
+   enabled = true
+   autoMounts = true
+}
+
+process {
+    withLabel: "jabs_classify" {
+        container = "/projects/kumar-lab/meta/images/JABS-behavior-classifier/headless/v0.37.0/latest.sif"
+    }
+    withLabel: "cpu" {
+        queue = "compute"
+        cpus = 1
+        memory = 24.GB
+        time = 24.h
+    }
+    withLabel: "highcpu" {
+        queue = "compute"
+        cpus = 16
+        memory = 64.GB
+        time = 24.h
+    }
+}
+
+executor {
+    name = 'slurm'
+    // The number of tasks the executor will handle in a parallel manner
+    queueSize = 24
+    submitRateLimit = '1 s'
+    // Determines the max rate of job submission per time unit, for example '10sec' eg. max 10 jobs per second or '1/2 s' i.e. 1 job submissions every 2 seconds.
+}