Merge pull request #289 from uclahs-cds/sfitz-update-resources

update resource allocations
uclahs-cds · May 15, 2024 · e038942 · e038942
2 parents e061aa5 + 1c02893
commit e038942
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Showing 8 changed files with 70 additions and 67 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Grant explicit permissions for Nextflow configuration test workflow
 - Update Nextflow configuration test workflows
 
+### Changed
+- Update resource allocations
+
 ## [8.0.0] - 2024-01-29
 
 ### Changed

diff --git a/config/F16.config b/config/F16.config
@@ -22,7 +22,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 3.GB
+                operand = 5.GB
             }
         }
     }
@@ -32,7 +32,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 3.GB
+                operand = 5.GB
             }
         }
     }
@@ -42,7 +42,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 3.GB
+                operand = 5.GB
             }
         }
     }
@@ -58,7 +58,7 @@ process {
     }
     withName: call_sSNV_Mutect2 {
         cpus = 1
-        memory = 3.GB
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -71,8 +71,8 @@ process {
         memory = 8.GB
         retry_strategy {
             memory {
-                strategy = 'exponential'
-                operand = 2
+                strategy = 'add'
+                operand = 20.GB
             }
         }
     }
@@ -88,11 +88,11 @@ process {
     }
     withName: run_sump_MuSE {
         cpus = 8
-        memory = 24.GB
+        memory = 16.GB
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 8.GB
+                operand = 16.GB
             }
         }
     }

diff --git a/config/F32.config b/config/F32.config
@@ -58,21 +58,21 @@ process {
     }
     withName: call_sSNV_Mutect2 {
         cpus = 1
-        memory = 3.GB
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 3.GB
+                operand = 2.GB
             }
         }
     }
     withName: run_LearnReadOrientationModel_GATK {
         cpus = 1
-        memory = 16.GB
+        memory = 12.GB
         retry_strategy {
             memory {
-                strategy = 'exponential'
-                operand = 2
+                strategy = 'add'
+                operand = 20.GB
             }
         }
     }
@@ -88,7 +88,7 @@ process {
     }
     withName: run_sump_MuSE {
         cpus = 12
-        memory = 48.GB
+        memory = 18.GB
         retry_strategy {
             memory {
                 strategy = 'add'

diff --git a/config/F72.config b/config/F72.config
@@ -8,7 +8,7 @@ process {
     }
     withName: call_sSNV_SomaticSniper {
         cpus = 1
-        memory = 1.GB
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -18,11 +18,11 @@ process {
     }
     withName: convert_BAM2Pileup_SAMtools {
         cpus = 1
-        memory = 1.GB
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 5.GB
+                operand = 16.GB
             }
         }
     }
@@ -68,11 +68,11 @@ process {
     }
     withName: run_LearnReadOrientationModel_GATK {
         cpus = 1
-        memory = 16.GB
+        memory = 12.GB
         retry_strategy {
             memory {
-                strategy = 'exponential'
-                operand = 2
+                strategy = 'add'
+                operand = 20.GB
             }
         }
     }
@@ -87,12 +87,12 @@ process {
         }
     }
     withName: run_sump_MuSE {
-        cpus = 24
-        memory = 80.GB
+        cpus = 12
+        memory = 18.GB
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 20.GB
+                operand = 24.GB
             }
         }
     }

diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
diff --git a/metadata.yaml b/metadata.yaml
@@ -1,6 +1,6 @@
 ---
 Category: 'pipeline'
-Description: 'A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.'
+Description: 'Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.'
 Maintainers: [[email protected]]
 Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon']
 Languages: ['Docker', 'Nextflow']

diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -113,7 +113,7 @@
           "memory": "6 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "3 GB",
+              "operand": "5 GB",
               "strategy": "add"
             }
           }
@@ -130,7 +130,7 @@
         },
         "call_sSNV_Mutect2": {
           "cpus": "1",
-          "memory": "3 GB",
+          "memory": "2 GB",
           "retry_strategy": {
             "memory": {
               "operand": "2 GB",
@@ -176,7 +176,7 @@
           "memory": "1 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "3 GB",
+              "operand": "5 GB",
               "strategy": "add"
             }
           }
@@ -186,7 +186,7 @@
           "memory": "1 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "3 GB",
+              "operand": "5 GB",
               "strategy": "add"
             }
           }
@@ -206,17 +206,17 @@
           "memory": "8 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "2",
-              "strategy": "exponential"
+              "operand": "20 GB",
+              "strategy": "add"
             }
           }
         },
         "run_sump_MuSE": {
           "cpus": "8",
-          "memory": "24 GB",
+          "memory": "16 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "8 GB",
+              "operand": "16 GB",
               "strategy": "add"
             }
           }
@@ -329,9 +329,9 @@
         "cpus": "6",
         "memory": {
           "1": "6 GB",
-          "2": "9 GB",
-          "3": "12 GB",
-          "closure": "retry_updater(6 GB, add, 3 GB, $task.attempt, memory)"
+          "2": "11 GB",
+          "3": "16 GB",
+          "closure": "retry_updater(6 GB, add, 5 GB, $task.attempt, memory)"
         }
       },
       "withName:call_sSNV_MuSE": {
@@ -346,10 +346,10 @@
       "withName:call_sSNV_Mutect2": {
         "cpus": "1",
         "memory": {
-          "1": "3 GB",
-          "2": "5 GB",
-          "3": "7 GB",
-          "closure": "retry_updater(3 GB, add, 2 GB, $task.attempt, memory)"
+          "1": "2 GB",
+          "2": "4 GB",
+          "3": "6 GB",
+          "closure": "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
         }
       },
       "withName:call_sSNV_SomaticSniper": {
@@ -386,18 +386,18 @@
         "cpus": "1",
         "memory": {
           "1": "1 GB",
-          "2": "4 GB",
-          "3": "7 GB",
-          "closure": "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+          "2": "6 GB",
+          "3": "11 GB",
+          "closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
         }
       },
       "withName:create_IndelCandidate_SAMtools": {
         "cpus": "1",
         "memory": {
           "1": "1 GB",
-          "2": "4 GB",
-          "3": "7 GB",
-          "closure": "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+          "2": "6 GB",
+          "3": "11 GB",
+          "closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
         }
       },
       "withName:plot_VennDiagram_R": {
@@ -413,18 +413,18 @@
         "cpus": "1",
         "memory": {
           "1": "8 GB",
-          "2": "16 GB",
+          "2": "28 GB",
           "3": "31 GB",
-          "closure": "retry_updater(8 GB, exponential, 2, $task.attempt, memory)"
+          "closure": "retry_updater(8 GB, add, 20 GB, $task.attempt, memory)"
         }
       },
       "withName:run_sump_MuSE": {
         "cpus": "8",
         "memory": {
-          "1": "24 GB",
+          "1": "16 GB",
           "2": "31 GB",
           "3": "31 GB",
-          "closure": "retry_updater(24 GB, add, 8 GB, $task.attempt, memory)"
+          "closure": "retry_updater(16 GB, add, 16 GB, $task.attempt, memory)"
         }
       },
       "withName:run_validate_PipeVal": {

diff --git a/test/configtest-F32.json b/test/configtest-F32.json
@@ -130,10 +130,10 @@
         },
         "call_sSNV_Mutect2": {
           "cpus": "1",
-          "memory": "3 GB",
+          "memory": "2 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "3 GB",
+              "operand": "2 GB",
               "strategy": "add"
             }
           }
@@ -203,17 +203,17 @@
         },
         "run_LearnReadOrientationModel_GATK": {
           "cpus": "1",
-          "memory": "16 GB",
+          "memory": "12 GB",
           "retry_strategy": {
             "memory": {
-              "operand": "2",
-              "strategy": "exponential"
+              "operand": "20 GB",
+              "strategy": "add"
             }
           }
         },
         "run_sump_MuSE": {
           "cpus": "12",
-          "memory": "48 GB",
+          "memory": "18 GB",
           "retry_strategy": {
             "memory": {
               "operand": "16 GB",
@@ -346,10 +346,10 @@
       "withName:call_sSNV_Mutect2": {
         "cpus": "1",
         "memory": {
-          "1": "3 GB",
-          "2": "6 GB",
-          "3": "9 GB",
-          "closure": "retry_updater(3 GB, add, 3 GB, $task.attempt, memory)"
+          "1": "2 GB",
+          "2": "4 GB",
+          "3": "6 GB",
+          "closure": "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
         }
       },
       "withName:call_sSNV_SomaticSniper": {
@@ -412,19 +412,19 @@
       "withName:run_LearnReadOrientationModel_GATK": {
         "cpus": "1",
         "memory": {
-          "1": "16 GB",
+          "1": "12 GB",
           "2": "32 GB",
-          "3": "64 GB",
-          "closure": "retry_updater(16 GB, exponential, 2, $task.attempt, memory)"
+          "3": "52 GB",
+          "closure": "retry_updater(12 GB, add, 20 GB, $task.attempt, memory)"
         }
       },
       "withName:run_sump_MuSE": {
         "cpus": "12",
         "memory": {
-          "1": "48 GB",
-          "2": "64 GB",
-          "3": "64 GB",
-          "closure": "retry_updater(48 GB, add, 16 GB, $task.attempt, memory)"
+          "1": "18 GB",
+          "2": "34 GB",
+          "3": "50 GB",
+          "closure": "retry_updater(18 GB, add, 16 GB, $task.attempt, memory)"
         }
       },
       "withName:run_validate_PipeVal": {