From 349f44aae7577665986e9b23c079662b38d6900e Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Tue, 7 Oct 2025 19:42:43 -0400
Subject: [PATCH 1/2] Update GENERATE_BEHAVIOR_TABLES to match updated
 generate-tables args

---
 nextflow/modules/jabs_classifiers.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/nextflow/modules/jabs_classifiers.nf b/nextflow/modules/jabs_classifiers.nf
index 6f9efc8..9c4162b 100644
--- a/nextflow/modules/jabs_classifiers.nf
+++ b/nextflow/modules/jabs_classifiers.nf
@@ -103,14 +103,22 @@ process GENERATE_BEHAVIOR_TABLES {
     tuple path("${in_pose.baseName}*_bouts.csv"), path("${in_pose.baseName}*_summaries.csv"), emit: files
 
     script:
+    def behaviorJson = groovy.json.JsonOutput.toJson([
+        behaviors: classifiers.collect { entry ->
+            [
+                behavior: entry.key,
+                stitch_gap: entry.value.stitch_value,
+                min_bout_length: entry.value.filter_value
+            ]
+        }
+    ])
     """
-    behavior_command="--behavior ${classifiers.collect { entry -> "$entry.key --stitch-gap $entry.value.stitch_value --min-bout-length $entry.value.filter_value" }.join(' --behavior ')}"
     jabs-postprocess generate-tables \
         --project-folder . \
         --feature-folder . \
         --out-prefix ${in_pose.baseName} \
         --out-bin-size 5 \
-        \${behavior_command}
+        --behavior-config '${behaviorJson}'
     """
 }
 

From f6f6a703e1f9b40b9e766e6e5d683f28742d58db Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Wed, 8 Oct 2025 14:03:31 -0400
Subject: [PATCH 2/2] Update jabs-postprocess image version

---
 nextflow/configs/profiles/sumner2.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow/configs/profiles/sumner2.config b/nextflow/configs/profiles/sumner2.config
index bc2e10f..8f79707 100644
--- a/nextflow/configs/profiles/sumner2.config
+++ b/nextflow/configs/profiles/sumner2.config
@@ -183,7 +183,7 @@ process {
         container = "/projects/kumar-lab/meta/images/JABS-behavior-classifier/headless/v0.36.1/latest.sif"
     }
     withLabel: "jabs_postprocess" {
-        container = "/projects/kumar-lab/meta/images/JABS-postprocess/jabs-postprocess/v0.3.1/latest.sif"
+        container = "/projects/kumar-lab/meta/images/JABS-postprocess/jabs-postprocess/v0.4.0/latest.sif"
     }
     withLabel: "jabs_table_convert" {
         container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/RBase/v0.1.2/latest.sif"