Varlociraptor integration

assets/varlociraptor_somatic_with_priors.yte.yaml

@@ -0,0 +1,34 @@
+species:
+  heterozygosity: 0.001
+  germline-mutation-rate: 1e-3
+  ploidy:
+    male:
+      all: 2
+      X: 1
+      Y: 1
+    female:
+      all: 2
+      X: 2
+      Y: 0
+  genome-size: 3.5e9
+
+samples:
+  tumor:
+    sex: ?sex_string
+    somatic-effective-mutation-rate: 1e-6
+    inheritance:
+      clonal:
+        from: normal
+        somatic: true
+    contamination:
+      by: normal
+      fraction: 0.1
+  normal:
+    sex: ?sex_string
+    somatic-effective-mutation-rate: 1e-10
+
+events:
+  somatic_tumor_high: "normal:0.0 & tumor:[0.1,1.0]"
+  somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
+  somatic_normal: "normal:]0.0,0.5["
+  germline: "normal:0.5 | normal:1.0"

conf/modules/post_variant_calling.config

@@ -84,4 +84,85 @@ process {
                 pattern: "*.tbi"
         ]
     }
+
+    withName: 'FILL_SCENARIO_FILE' {
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
+        ]
+    }
+
+    withName: 'ALIGNMENTPROPERTIES_NORMAL' {
+        ext.prefix = { "${meta.normal_id}" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
+        ]
+    }
+
+    withName: 'VCFSPLIT_NORMAL' {
+        ext.prefix = { "${meta.normal_id}.${meta.variantcaller}.split" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
+        ]
+    }
+
+    withName: 'PREPROCESS_NORMAL' {
+        ext.prefix = { "${meta.normal_id}.${meta.variantcaller}.preprocess.${meta.chunk}" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
+        ]
+    }
+
+    withName: 'ALIGNMENTPROPERTIES_TUMOR' {
+        ext.prefix = { "${meta.tumor_id}" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
+        ]
+    }
+
+    withName: 'VCFSPLIT_TUMOR' {
+        ext.prefix = { "${meta.tumor_id}.${meta.variantcaller}.split" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
+        ]
+    }
+
+    withName: 'PREPROCESS_TUMOR' {
+        ext.prefix = { "${meta.tumor_id}.${meta.variantcaller}.preprocess.${meta.chunk}" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
+        ]
+    }
+
+    withName: 'VARLOCIRAPTOR_CALLVARIANTS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.call.${meta.chunk}" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
+        ]
+    }
+
+    withName: 'SORT_CALLED_CHUNKS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" }
+        ext.args   = { '--output-type z --write-index=tbi' }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
+        ]
+    }
+
+    withName: 'MERGE_CALLED_CHUNKS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.varlociraptor" }
+        ext.args   = { '--allow-overlaps --output-type z --write-index=tbi' }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/varlociraptor/" },
+        ]
+    }
 }

modules.json

@@ -377,6 +377,11 @@
                         "git_sha": "083667c2f0d3b57aa373ffa8891d04b3c839b0b4",
                         "installed_by": ["modules"]
                     },
+                    "rbt/vcfsplit": {
+                        "branch": "master",
+                        "git_sha": "3e5034548e2398b006a9e01fb82673ffa5c83d9f",
+                        "installed_by": ["modules"]
+                    },
                     "samblaster": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
@@ -527,10 +532,30 @@
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
+                    "varlociraptor/callvariants": {
+                        "branch": "master",
+                        "git_sha": "b0a35d996f6140f18e040099c94ffc0c0f005187",
+                        "installed_by": ["modules"]
+                    },
+                    "varlociraptor/estimatealignmentproperties": {
+                        "branch": "master",
+                        "git_sha": "b0a35d996f6140f18e040099c94ffc0c0f005187",
+                        "installed_by": ["modules"]
+                    },
+                    "varlociraptor/preprocess": {
+                        "branch": "master",
+                        "git_sha": "b0a35d996f6140f18e040099c94ffc0c0f005187",
+                        "installed_by": ["modules"]
+                    },
                     "vcftools": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
+                    },
+                    "yte": {
+                        "branch": "master",
+                        "git_sha": "87169022c82b7ad5357302ad5b438fc586c3d471",
+                        "installed_by": ["modules"]
                     }
                 }
             },