From ff27b0d4e20e8ecaa319bd59d0422423b0c27fd6 Mon Sep 17 00:00:00 2001
From: Brian Geuther <Brian.Geuther@jax.org>
Date: Wed, 24 Sep 2025 14:57:31 -0400
Subject: [PATCH 1/2] Config changes being used for SFARI that might be
 affecting single-mouse

---
 nextflow/configs/profiles/sumner2.config | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/nextflow/configs/profiles/sumner2.config b/nextflow/configs/profiles/sumner2.config
index 6aeefde..1313b8b 100644
--- a/nextflow/configs/profiles/sumner2.config
+++ b/nextflow/configs/profiles/sumner2.config
@@ -192,7 +192,8 @@ process {
      * Runtime options
      */
     withLabel: "tracking" {
-        container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/deployment-runtime_2025-08-26.sif"
+        container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/deployment-runtime_2025-08-28.sif"
+        model_dir = "/projects/kumar-lab/multimouse-pipeline/nextflow-artifacts/neural_net_models/"
     }
     withLabel: "jabs_classify" {
         container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/JABS-GUI_2025-02-12_v0.18.1.sif"
@@ -218,6 +219,11 @@ process {
     withLabel: "rclone" {
         // executor.queueSize = 1
         container = "/projects/kumar-lab/multimouse-pipeline/rclone_2025-08-18.sif"
+        cpus = 1
+        time = '48h'
+        memory = '12GB'
+        queue = 'xfer'
+        clusterOptions = '-q xfer'
     }
 
     /* 
@@ -452,8 +458,11 @@ process {
         cpus = 2
         // 8.53 GB * num_mice
         memory = {
-            def r_value = Math.max(1, ((8.53 * params.num_mice) * 2.5 * task.attempt).toInteger())
-            return r_value + '.GB'
+            def per_mouse_gb = 10
+            def base = params.num_mice * per_mouse_gb
+            def retry_factor = 1 + (0.5 * (task.attempt - 1))
+            def uncapped_memory = (base * retry_factor).toInt
+            return Math.min(uncapped_memory, 128) + '.GB'
         }
         time = { 5.hours * task.attempt }
         array = 200
@@ -493,7 +502,7 @@ process {
         // TODO: Tune these numbers based on number of mice
         // First video suggested ~16GB and ~30min for 3 mice
         memory = { 16.GB * task.attempt }
-        time = { 45.min * task.attempt }
+        time = { 2.hours * task.attempt }
         array = 200
         errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
         maxRetries = 3
@@ -510,7 +519,7 @@ process {
     }
     withLabel: "r_food_hopper" {
         cpus = 2
-        memory = { 4.GB * task.attempt }
+        memory = { 8.GB * task.attempt }
         time = { 10.min * task.attempt }
         array = 200
         errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }

From ebb7127319eb615026cc4accf8ec82c7149f0cd8 Mon Sep 17 00:00:00 2001
From: Brian Geuther <Brian.Geuther@jax.org>
Date: Thu, 2 Oct 2025 11:37:03 -0400
Subject: [PATCH 2/2] Adjusting tags for modules

---
 nextflow/modules/jabs_classifiers.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nextflow/modules/jabs_classifiers.nf b/nextflow/modules/jabs_classifiers.nf
index 147b054..8d5341b 100644
--- a/nextflow/modules/jabs_classifiers.nf
+++ b/nextflow/modules/jabs_classifiers.nf
@@ -154,6 +154,7 @@ process PREDICT_HEURISTICS {
  */
 process BEHAVIOR_TABLE_TO_FEATURES {
     label "jabs_table_convert"
+    label "cpu"
     label "r_jabs_table_convert"
 
     input:
@@ -183,7 +184,8 @@ process BEHAVIOR_TABLE_TO_FEATURES {
 * @publish ./results/merged_behavior_tables Merge log file
 */
 process AGGREGATE_BOUT_TABLES {
-    label "jabs_table_convert"
+    label "jabs_postprocess"
+    label "cpu"
     label "r_jabs_table_convert"
 
     publishDir "${params.pubdir}/merged_behavior_tables", mode: 'copy'