update deepvariant module (genomic-medicine-sweden#93)

fellen31 · Apr 22, 2024 · 3933fb7 · 3933fb7
1 parent 71d55cb
commit 3933fb7
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Showing 12 changed files with 583 additions and 60 deletions.
diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
@@ -26,10 +26,19 @@ process {
 
     withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT' {
 
-        if(params.preset == 'revio' | params.preset == 'pacbio') {
-            ext.model_type = 'PACBIO'
-        } else if(params.preset == 'ONT_R10') {
-            ext.model_type = 'ONT_R104'
+        ext.prefix = { intervals ? "${meta.id}" + "_" + "${intervals.getSimpleName()}" + "_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(' ') }
         }
     }
 

diff --git a/modules.json b/modules.json
@@ -41,6 +41,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "deepvariant": {
+                        "branch": "master",
+                        "git_sha": "199ba086a259e1933d6e0ab7596e4a977bbd483a",
+                        "installed_by": ["modules"]
+                    },
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae",

diff --git a/modules/local/google/deepvariant.nf b/modules/local/google/deepvariant.nf
diff --git a/modules/nf-core/deepvariant/README.md b/modules/nf-core/deepvariant/README.md
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml
diff --git a/modules/nf-core/deepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/tests/main.nf.test