Merge branch 'dev' into remove-extra-gvcfs

genomic-medicine-sweden · Jul 1, 2024 · db25100 · db25100
2 parents d5114d3 + 18d1eb0
commit db25100
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Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#230](https://github.com/genomic-medicine-sweden/nallo/pull/230) - Added nf-test to the short variant calling workflow
+- [#234](https://github.com/genomic-medicine-sweden/nallo/pull/234) - Added a `--deepvariant_model_type` parameter to override the model type set by `--preset`
 
 ### `Changed`
 
@@ -20,9 +21,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-| Old parameter   | New parameter |
-| --------------- | ------------- |
-| `--extra_gvcfs` |               |
+### Parameters
+
+| Old parameter   | New parameter              |
+| --------------- | -------------------------- |
+|                 | `--deepvariant_model_type` |
+| `--extra_gvcfs` |                            |
+
 
 ## v0.2.0 - [2024-06-26]
 

diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
@@ -27,18 +27,11 @@ process {
     withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT' {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
 
-        if(params.preset.matches('revio|pacbio')) {
-            ext.args = { [
-                "--sample_name=${meta.id}",
-                '--model_type=PACBIO',
-                ].join(' ') }
-
-        } else if(params.preset.matches('ONT_R10')) {
-            ext.args = { [
-                "--sample_name=${meta.id}",
-                '--model_type=ONT_R104',
-                ].join(' ') }
-        }
+        ext.args = { [
+            "--sample_name=${meta.id}",
+            "--model_type=${params.deepvariant_model_type}",
+            ].join(' ') }
+
     }
 
     withName: '.*:SHORT_VARIANT_CALLING:GLNEXUS' {

diff --git a/nextflow.config b/nextflow.config
@@ -22,6 +22,7 @@ params {
     hificnv_xx                 = null
     hificnv_exclude            = null
     somalier_sites             = null
+    deepvariant_model_type     = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO'
 
     // Skip parts of the workflow
     skip_raw_read_qc           = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -368,6 +368,13 @@
                     "type": "integer",
                     "default": 110,
                     "description": "VEP cache version"
+                },
+                "deepvariant_model_type": {
+                    "type": "string",
+                    "default": "PACBIO",
+                    "description": "Sets the model type for DeepVariant",
+                    "hidden": true,
+                    "enum": ["PACBIO", "ONT_R104"]
                 }
             },
             "required": ["preset"]