diff --git a/nextflow/configs/profiles/sumner2.config b/nextflow/configs/profiles/sumner2.config index cceacfc..7c35754 100644 --- a/nextflow/configs/profiles/sumner2.config +++ b/nextflow/configs/profiles/sumner2.config @@ -251,7 +251,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_fboli_predict" { @@ -263,7 +263,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // Frailty Resources @@ -280,7 +280,7 @@ process { return r_value + '.min' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_rearpaw" { @@ -292,7 +292,7 @@ process { } time = { 10.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // Gait Resources @@ -305,7 +305,7 @@ process { } time = { 10.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_gait_bin" { @@ -317,7 +317,7 @@ process { } time = { 5.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // JABS Resources @@ -337,7 +337,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_jabs_classify" { @@ -355,7 +355,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_jabs_tablegen" { @@ -363,7 +363,7 @@ process { memory = { 1.GB * task.attempt } time = { 5.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_jabs_heuristic" { @@ -377,7 +377,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_jabs_table_convert" { @@ -387,7 +387,7 @@ process { // High value in experiments was 1-minute for a 1-hr video time = { 20.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // Single Mouse Resources @@ -407,7 +407,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_single_keypoints" { @@ -418,7 +418,7 @@ process { memory = { 64.GB * task.attempt } time = { 6.hours * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_single_qc" { @@ -426,7 +426,7 @@ process { cpus = 1 memory = { 4.GB * task.attempt } time = { 20.min * task.attempt } - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_clip_video" { @@ -442,7 +442,7 @@ process { return r_value + '.sec' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // Multi Mouse Resources @@ -456,7 +456,7 @@ process { } time = { 5.hours * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_multi_keypoints" { @@ -472,7 +472,7 @@ process { return r_value + '.hours' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_multi_identity" { @@ -484,7 +484,7 @@ process { return r_value + '.hours' } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_multi_tracklets" { @@ -493,6 +493,9 @@ process { // First video suggested ~16GB and ~30min for 3 mice memory = { 16.GB * task.attempt } time = { 45.min * task.attempt } + array = 200 + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } + maxRetries = 3 } // Static Object Resources // These do not scale with clip duration @@ -501,7 +504,7 @@ process { memory = { 4.GB * task.attempt } time = { 10.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_food_hopper" { @@ -509,7 +512,7 @@ process { memory = { 4.GB * task.attempt } time = { 10.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_lixit" { @@ -517,7 +520,7 @@ process { memory = { 4.GB * task.attempt } time = { 10.min * task.attempt } array = 200 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } // Utility Resources @@ -526,14 +529,14 @@ process { memory = { 1.GB * task.attempt } time = { 5.min * task.attempt } array = 500 - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } withLabel: "r_gen_vid" { cpus = 1 memory = { 1.GB * task.attempt } time = { 1.hours * task.attempt } - errorStrategy = 'retry' + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } maxRetries = 3 } }