Update main workflow with changes to single_mouse_classifier objects

Author: bergsalex

nextflow/configs/profiles/sumner2.config

@@ -2,6 +2,8 @@
 
 workDir = "/flashscratch/${USER}/nextflow-work"
 
+includeConfig { "/projects/kumar-lab/data/jabs/classifiers/v0.37.0/latest.config" }
+
 params {
     /*
      * Additional Parameters for the sumner2 profile
@@ -14,10 +16,6 @@ params {
      * - filter_processed: whether to filter processed files in the batch
 
      * - jabs_version: version of JABS used for the classifiers
-     * - classifier_project_folders: directory containing the classifier project folders
-     * - classifier_training_file_folder: directory containing the classifier training files
-     * - exported_classifier_folder: directory containing the exported classifiers
-     * - classifier_artifact_suffix: suffix for the classifier artifacts
      * - classifier_window_sizes: window sizes cached for use in classifiers
      * - single_mouse_classifiers: classifiers for single mouse behavior. Each classifier is described as
          behavior name (identical key used in JABS): [
@@ -37,75 +35,10 @@ params {
     heuristic_classifier_folder = "/JABS-postprocess/heuristic_classifiers/"
     filter_processed = false
 
-    jabs_version = "0.18.1"
-    classifier_project_folders = "/projects/kumar-lab/multimouse-pipeline/nextflow-artifacts/project_folders/"
-    classifier_training_file_folder = "/projects/kumar-lab/multimouse-pipeline/nextflow-artifacts/training_files/"
-    exported_classifier_folder = "/projects/kumar-lab/multimouse-pipeline/nextflow-artifacts/exported_classifiers/"
-    classifier_artifact_suffix = "_classifier_v${jabs_version}.pickle"
+    jabs_version = "v0.37.0"
     classifier_window_sizes = [2, 5, 10, 20, 30, 60]
     // Classifiers are described as behavior_name: project_folder
-    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,
-        ],
-        // "Jerk": [  // Needs to be re-exported to remove static object features (unavailable for single mouse)
-        //     "project_folder_name": "social-play",
-        //     "stitch_value": 1,
-        //     "filter_value": 6,
-        // ]
-    ]
+
     heuristic_classifiers = ["corner", "corner_facing", "freeze", "locomotion", "periphery", "wall_facing"]
 
     // Number of 5-minute bins for transforming summary tables into bins

nextflow/modules/jabs_classifiers.nf

@@ -67,10 +67,9 @@ process PREDICT_CLASSIFIERS {
 
     script:
     """
-    for classifier in ${classifiers.keySet().collect { params.exported_classifier_folder + it + params.classifier_artifact_suffix }.join(' ')};
+    for classifier_path in ${classifiers.collect { _behavior, details -> details.classifier_path }.join(' ')};
     do
-        ln -s \${classifier} .
-        jabs-classify classify --classifier \$(basename \${classifier}) --input-pose ${in_pose} --out-dir . --feature-dir .
+        jabs-classify classify --classifier "\${classifier_path}" --input-pose ${in_pose} --out-dir . --feature-dir .
     done
     """
 }