update M64 resources

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Update Nextflow configuration test workflows
 
 ### Changed
+- Update M64 resource allocations
 - Update resource allocations
 
 ## [8.0.0] - 2024-01-29

config/M64.config

@@ -9,87 +9,115 @@ process {
     if (params.input_type == 'bam') {
         withName: call_sSNV_SomaticSniper {
             cpus = 1
-            memory = 316.GB
+            memory = 20.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 20.GB
+                }
+            }
         }
         withName: convert_BAM2Pileup_SAMtools {
             cpus = 1
-            memory = 316.GB
+            memory = 100.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 100.GB
+                }
+            }
         }
         withName: create_IndelCandidate_SAMtools {
             cpus = 1
-            memory = 316.GB
+            memory = 10.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 10.GB
+                }
+            }
+        }
+        withName: generate_ReadCount_bam_readcount {
+            cpus = 1
+            memory = 20.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 20.GB
+                }
+            }
         }
         withName: call_sIndel_Manta {
-            cpus = 36
-            memory = 15.GB
+            cpus = 8
+            memory = 10.GB
             retry_strategy {
                 memory {
                     strategy = 'add'
-                    operand = 5.GB
+                    operand = 10.GB
                 }
             }
         }
         withName: call_sSNV_Strelka2 {
-            cpus = 36
-            memory = 10.GB
+            cpus = 28
+            memory = 30.GB
             retry_strategy {
                 memory {
                     strategy = 'add'
-                    operand = 5.GB
+                    operand = 30.GB
                 }
             }
         }
         withName: call_sSNV_Mutect2 {
-            cpus = 2
-            memory = 5.GB
+            cpus = 1
+            memory = 30.GB
             retry_strategy {
                 memory {
                     strategy = 'add'
-                    operand = 5.GB
+                    operand = 30.GB
                 }
             }
         }
         withName: run_LearnReadOrientationModel_GATK {
-            cpus = 4
-            memory = 8.GB
+            cpus = 1
+            memory = 30.GB
             retry_strategy {
                 memory {
-                    strategy = 'exponential'
-                    operand = 2
+                    strategy = 'add'
+                    operand = 30.GB
                 }
             }
         }
         withName: call_sSNV_MuSE {
             cpus = 16
-            memory = 128.GB
+            memory = 120.GB
             retry_strategy {
                 memory {
                     strategy = 'add'
-                    operand = 10.GB
+                    operand = 60.GB
                 }
             }
         }
         withName: run_sump_MuSE {
-            cpus = 2
-            memory = 128.GB
+            cpus = 6
+            memory = 40.GB
             retry_strategy {
                 memory {
                     strategy = 'add'
-                    operand = 10.GB
+                    operand = 20.GB
                 }
             }
         }
     }
     withName: plot_VennDiagram_R {
-    cpus = 1
-    memory = 1.GB
-    retry_strategy {
-        memory {
-            strategy = 'add'
-            operand = 10.GB
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
         }
     }
-    }
     withName: concat_VCFs_BCFtools {
         cpus = 1
         memory = 1.GB

config/template.config

@@ -15,7 +15,6 @@ params {
     reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
     intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
     output_dir = ''
-    work_dir = ''
     dataset_id = ''
     // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE