Merge pull request #239 from uclahs-cds/sfitz-release-7.0.0-rc2

Sfitz release 7.0.0 rc2 and resource allocation update
uclahs-cds · Oct 7, 2023 · c32a73f · c32a73f
2 parents 116049a + 59dbbf9
commit c32a73f
Show file tree

Hide file tree

Showing 5 changed files with 79 additions and 40 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,11 +6,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [7.0.0-rc.2] - 2023-10-05
+
 ### Added
 - Add .github/CODEOWNERS
 - Add check for MuSE or Mutect2 on F2 node
 
 ### Changed
+- Resource allocations changed for F32 and F72
 - Update `MuSE` to `v2.0.3`
 - Reorder all VCFs before intersection
 - Move `filter_VCF_BCFtools` to `common.nf`

diff --git a/config/F32.config b/config/F32.config
@@ -8,19 +8,37 @@ process {
     }
     withName: call_sSNV_SomaticSniper {
         cpus = 1
-        memory = 10.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: convert_BAM2Pileup_SAMtools {
         cpus = 1
-        memory = 10.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: create_IndelCandidate_SAMtools {
         cpus = 1
-        memory = 10.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: call_sIndel_Manta {
-        cpus = 32
-        memory = 15.GB
+        cpus = 8
+        memory = 6.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -29,8 +47,8 @@ process {
         }
     }
     withName: call_sSNV_Strelka2 {
-        cpus = 32
-        memory = 15.GB
+        cpus = 8
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -39,8 +57,8 @@ process {
         }
     }
     withName: call_sSNV_Mutect2 {
-        cpus = 2
-        memory = 5.GB
+        cpus = 1
+        memory = 3.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -59,7 +77,7 @@ process {
         }
     }
     withName: call_sSNV_MuSE {
-        cpus = 20
+        cpus = 12
         memory = 48.GB
         retry_strategy {
             memory {
@@ -69,7 +87,7 @@ process {
         }
     }
     withName: run_sump_MuSE {
-        cpus = 10
+        cpus = 12
         memory = 48.GB
         retry_strategy {
             memory {

diff --git a/config/F72.config b/config/F72.config
@@ -8,19 +8,37 @@ process {
     }
     withName: call_sSNV_SomaticSniper {
         cpus = 1
-        memory = 45.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: convert_BAM2Pileup_SAMtools {
         cpus = 1
-        memory = 45.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: create_IndelCandidate_SAMtools {
         cpus = 1
-        memory = 45.GB
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 5.GB
+            }
+        }
     }
     withName: call_sIndel_Manta {
-        cpus = 36
-        memory = 15.GB
+        cpus = 8
+        memory = 6.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -29,8 +47,8 @@ process {
         }
     }
     withName: call_sSNV_Strelka2 {
-        cpus = 36
-        memory = 10.GB
+        cpus = 8
+        memory = 2.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -39,12 +57,12 @@ process {
         }
     }
     withName: call_sSNV_Mutect2 {
-        cpus = 2
-        memory = 5.GB
+        cpus = 1
+        memory = 3.GB
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 5.GB
+                operand = 3.GB
             }
         }
     }
@@ -59,7 +77,7 @@ process {
         }
     }
     withName: call_sSNV_MuSE {
-        cpus = 20
+        cpus = 12
         memory = 60.GB
         retry_strategy {
             memory {
@@ -69,8 +87,8 @@ process {
         }
     }
     withName: run_sump_MuSE {
-        cpus = 10
-        memory = 70.GB
+        cpus = 24
+        memory = 80.GB
         retry_strategy {
             memory {
                 strategy = 'add'

diff --git a/main.nf b/main.nf
@@ -132,10 +132,10 @@ Channel
         }
     .set { normal_input }
 
-    script_dir_ch = Channel.fromPath(
-        "$projectDir/r-scripts",
-        checkIfExists: true
-        )
+script_dir_ch = Channel.fromPath(
+    "$projectDir/r-scripts",
+    checkIfExists: true
+    )
 
 workflow {
     reference_ch = Channel.from(
@@ -208,17 +208,6 @@ workflow {
             strelka2.out.gzvcf.set { strelka2_gzvcf_ch }
             strelka2.out.idx.set { strelka2_idx_ch }
         }
-    if ('mutect2' in params.algorithm) {
-        mutect2(
-            tumor_input.tumor_bam.collect(),
-            tumor_input.tumor_index.collect(),
-            normal_input.normal_bam.collect(),
-            normal_input.normal_index.collect(),
-            tumor_input.contamination_est.collect()
-            )
-            mutect2.out.gzvcf.set { mutect2_gzvcf_ch }
-            mutect2.out.idx.set { mutect2_idx_ch }
-        }
     if ('muse' in params.algorithm) {
         muse(
             tumor_input.tumor_bam,
@@ -231,6 +220,17 @@ workflow {
             muse.out.gzvcf.set { muse_gzvcf_ch }
             muse.out.idx.set { muse_idx_ch }
         }
+    if ('mutect2' in params.algorithm) {
+        mutect2(
+            tumor_input.tumor_bam.collect(),
+            tumor_input.tumor_index.collect(),
+            normal_input.normal_bam.collect(),
+            normal_input.normal_index.collect(),
+            tumor_input.contamination_est.collect()
+            )
+            mutect2.out.gzvcf.set { mutect2_gzvcf_ch }
+            mutect2.out.idx.set { mutect2_idx_ch }
+        }
 
     // Intersect all vcf files
     if (params.algorithm.size() > 1) {

diff --git a/nextflow.config b/nextflow.config
@@ -9,6 +9,6 @@ manifest {
     nextflowVersion = '>=20.07.1'
     author = 'Yuan Zhe (Caden) Bugh, Mao Tian, Sorel Fitz-Gibbon'
     homePage = 'https://github.com/uclahs-cds/pipeline-call-sSNV'
-    version = '7.0.0-rc.1'
+    version = '7.0.0-rc.2'
     name = 'call-sSNV'
 }