Merge pull request #274 from uclahs-cds/sfitz-input-vcfs

Sfitz input vcfs
uclahs-cds · May 30, 2024 · e27b4e7 · e27b4e7
2 parents 7dbc60c + f61eb0f
commit e27b4e7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+- Add `a_mini-all-tools-vcf-input` to `nftest`
+- Add option to input VCFs for intersection
 
 ## [8.1.0] - 2024-05-15
 

diff --git a/config/F16.config b/config/F16.config
@@ -6,99 +6,101 @@ process {
         cpus = 1
         memory = 1.GB
     }
-    withName: call_sSNV_SomaticSniper {
-        cpus = 1
-        memory = 1.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 3.GB
+    if (params.input_type == 'bam') {
+        withName: call_sSNV_SomaticSniper {
+            cpus = 1
+            memory = 1.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 3.GB
+                }
             }
         }
-    }
-    withName: convert_BAM2Pileup_SAMtools {
-        cpus = 1
-        memory = 1.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 5.GB
+        withName: convert_BAM2Pileup_SAMtools {
+            cpus = 1
+            memory = 1.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 5.GB
+                }
             }
         }
-    }
-    withName: create_IndelCandidate_SAMtools {
-        cpus = 1
-        memory = 1.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 5.GB
+        withName: create_IndelCandidate_SAMtools {
+            cpus = 1
+            memory = 1.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 5.GB
+                }
             }
         }
-    }
-    withName: call_sIndel_Manta {
-        cpus = 6
-        memory = 6.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 5.GB
+        withName: call_sIndel_Manta {
+            cpus = 6
+            memory = 6.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 5.GB
+                }
             }
-        }
-    }
-    withName: call_sSNV_Strelka2 {
-        cpus = 6
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 12.GB
+            withName: call_sSNV_Strelka2 {
+                cpus = 6
+                memory = 2.GB
+                retry_strategy {
+                    memory {
+                        strategy = 'add'
+                        operand = 12.GB
+                    }
+                }
             }
         }
-    }
-    withName: call_sSNV_Mutect2 {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 2.GB
+        withName: call_sSNV_Mutect2 {
+            cpus = 1
+            memory = 2.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 2.GB
+                }
             }
         }
-    }
-    withName: run_LearnReadOrientationModel_GATK {
-        cpus = 1
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 20.GB
+        withName: run_LearnReadOrientationModel_GATK {
+            cpus = 1
+            memory = 8.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 20.GB
+                }
             }
-        }
-    }
-    withName: call_sSNV_MuSE {
-        cpus = 6
-        memory = 24.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 8.GB
+            withName: call_sSNV_MuSE {
+                cpus = 6
+                memory = 24.GB
+                retry_strategy {
+                    memory {
+                        strategy = 'add'
+                        operand = 8.GB
+                    }
+                }
             }
         }
-    }
-    withName: run_sump_MuSE {
-        cpus = 8
-        memory = 16.GB
-        retry_strategy {
-            memory {
-                strategy = 'add'
-                operand = 16.GB
+        withName: run_sump_MuSE {
+            cpus = 8
+            memory = 16.GB
+            retry_strategy {
+                memory {
+                    strategy = 'add'
+                    operand = 16.GB
+                }
             }
         }
     }
     withName: plot_VennDiagram_R {
-        cpus = 2
-        memory = 5.GB
+        cpus = 1
+        memory = 1.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -107,8 +109,8 @@ process {
         }
     }
     withName: concat_VCFs_BCFtools {
-        cpus = 2
-        memory = 5.GB
+        cpus = 1
+        memory = 1.GB
         retry_strategy {
             memory {
                 strategy = 'add'

diff --git a/config/F2.config b/config/F2.config
@@ -8,28 +8,30 @@ process {
         cpus = 1
         memory = 1500.MB
     }
-    withName: call_sSNV_SomaticSniper {
-        cpus = 1
-        memory = 1500.MB
-    }
-    withName: convert_BAM2Pileup_SAMtools {
-        cpus = 1
-        memory = 1500.MB
-    }
-    withName: create_IndelCandidate_SAMtools {
-        cpus = 1
-        memory = 1500.MB
-    }
-    withName: call_sIndel_Manta {
-        cpus = 2
-    }
-    withName: call_sSNV_Strelka2 {
-        cpus = 2
+    if (params.input_type == 'bam') {
+        withName: call_sSNV_SomaticSniper {
+            cpus = 1
+            memory = 1500.MB
+        }
+        withName: convert_BAM2Pileup_SAMtools {
+            cpus = 1
+            memory = 1500.MB
+        }
+        withName: create_IndelCandidate_SAMtools {
+            cpus = 1
+            memory = 1500.MB
+        }
+        withName: call_sIndel_Manta {
+            cpus = 2
+        }
+        withName: call_sSNV_Strelka2 {
+            cpus = 2
+        }
     }
     withName: plot_VennDiagram_R {
-        cpus = 2
+        cpus = 1
     }
     withName: concat_VCFs_BCFtools {
-        cpus = 2
+        cpus = 1
     }
 }