Nf-core lint clearing

oist · May 15, 2024 · 7943e4b · 7943e4b
1 parent 8b496ff
commit 7943e4b
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Showing 3 changed files with 31 additions and 20 deletions.
diff --git a/modules.json b/modules.json
@@ -82,7 +82,9 @@
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
@@ -95,4 +97,4 @@
             }
         }
     }
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -65,7 +65,7 @@ params {
     // Alignment options
     lastal_args                = 'C2'
     lastal_extr_args           = 'D1e9'
-    last_split_mismap          = '1e-5'
+    last_split_mismap          = '1e-05'
 
     // Schema validation default options
     validationFailUnrecognisedParams = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -357,6 +357,29 @@
                     "hidden": true
                 }
             }
+        },
+        "new_group_1": {
+            "title": "New Group 1",
+            "type": "object",
+            "description": "Lastal, last split arguments",
+            "default": "",
+            "properties": {
+                "lastal_args": {
+                    "type": "string",
+                    "default": "C2",
+                    "description": "this defaults to -C2 and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial."
+                },
+                "lastal_extr_args": {
+                    "type": "string",
+                    "default": "D1e9",
+                    "description": "(default: -D1e9) is only passed to lastal and can be used for arguments that are not recognised by last-train."
+                },
+                "last_split_mismap": {
+                    "type": "string",
+                    "default": 1e-05,
+                    "description": "By default, last-split runs with -m1e-5 to omit alignments with mismap probability > 10\u22125, but this can be overriden with the --last_split_mismap option."
+                }
+            }
         }
     },
     "allOf": [
@@ -383,23 +406,9 @@
         },
         {
             "$ref": "#/definitions/generic_options"
-        }
-    ],
-    "properties": {
-        "lastal_args": {
-            "type": "string",
-            "default": "C2",
-            "description": "this defaults to -C2 and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial."
-        },
-        "lastal_extr_args": {
-            "type": "string",
-            "default": "D1e9",
-            "description": "(default: -D1e9) is only passed to lastal and can be used for arguments that are not recognised by last-train."
         },
-        "last_split_mismap": {
-            "type": "string",
-            "default": 1e-05,
-            "description": "By default, last-split runs with -m1e-5 to omit alignments with mismap probability > 10\u22125, but this can be overriden with the --last_split_mismap option."
+        {
+            "$ref": "#/definitions/new_group_1"
         }
-    }
+    ]
 }