fix resourceLimits

nf-core · Oct 17, 2024 · 9fb3903 · 9fb3903
1 parent 4e3cef0
commit 9fb3903
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Showing 5 changed files with 30 additions and 23 deletions.
diff --git a/conf/test_screening.config b/conf/test_screening.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test screening profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input                      = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test.csv"
     analysis                   = 'screening'
@@ -37,4 +32,9 @@ process {
     withName: BAGEL2_BF {
         ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
     }
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
 }
diff --git a/conf/test_screening_count_table.config b/conf/test_screening_count_table.config
@@ -9,16 +9,18 @@
 
 ----------------------------------------------------------------------------------------
 */
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
 params {
     config_profile_name        = 'Test screening profile with an input count table'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     count_table       = params.pipelines_testdata_base_path + "crisprseq/testdata/count_table.tsv"
     analysis          = 'screening'

diff --git a/conf/test_screening_paired.config b/conf/test_screening_paired.config
@@ -14,10 +14,6 @@ params {
     config_profile_name        = 'Test screening profile paired-end'
     config_profile_description = 'Minimal test dataset to check pipeline function for paired-end data'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
 
     // Input data
     input             = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test_paired.csv"
@@ -29,4 +25,9 @@ process {
     withName: BAGEL2_BF {
         ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
     }
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
 }
diff --git a/conf/test_screening_rra.config b/conf/test_screening_rra.config
@@ -14,10 +14,6 @@ params {
     config_profile_name        = 'Test screening profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
 
     // Input data
     input                      = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test.csv"
@@ -34,4 +30,9 @@ process {
     withName: BAGEL2_BF {
         ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
     }
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
 }
diff --git a/conf/test_umis.config b/conf/test_umis.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test profile UMIs'
     config_profile_description = 'Minimal test dataset to check pipeline function with UMIs option'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input          = params.pipelines_testdata_base_path + "crisprseq/testdata-edition/samplesheet_test_umis.csv"
     analysis       = 'targeted'
@@ -27,3 +22,11 @@ params {
     // Aligner
     aligner = 'minimap2'
 }
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}