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Klaus 277 bug patches #91

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Merged
SkepticRaven merged 3 commits into from
Oct 3, 2025
Merged

Klaus 277 bug patches #91

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ff27b0d
Config changes being used for SFARI that might be affecting single-mouse
SkepticRaven Sep 24, 2025
5f2496f
Merge branch 'main' into KLAUS-277-bug-patches
SkepticRaven Oct 2, 2025
ebb7127
Adjusting tags for modules
SkepticRaven Oct 2, 2025
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16 changes: 12 additions & 4 deletions nextflow/configs/profiles/sumner2.config
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Original file line number Diff line number Diff line change
Expand Up @@ -218,6 +218,11 @@ 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'
}

/*
Expand Down Expand Up @@ -452,8 +457,11 @@ 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
Expand Down Expand Up @@ -493,7 +501,7 @@ 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
Expand All @@ -510,7 +518,7 @@ 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' }
Expand Down
4 changes: 3 additions & 1 deletion nextflow/modules/jabs_classifiers.nf
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Expand Up @@ -154,6 +154,7 @@ process PREDICT_HEURISTICS {
*/
process BEHAVIOR_TABLE_TO_FEATURES {
label "jabs_table_convert"
label "cpu"
label "r_jabs_table_convert"

input:
Expand Down Expand Up @@ -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'
Expand Down