diff --git a/nextflow/configs/profiles/sumner2.config b/nextflow/configs/profiles/sumner2.config index 33d6988..da11354 100644 --- a/nextflow/configs/profiles/sumner2.config +++ b/nextflow/configs/profiles/sumner2.config @@ -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' } /* @@ -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 @@ -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 @@ -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' } 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'