updated linting

nf-cmgg · Dec 12, 2022 · 2e4d5c9 · 2e4d5c9
1 parent db09c67
commit 2e4d5c9
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -7,6 +7,7 @@ lint:
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
+    - lib/WorkflowNf-cmgg-germline.groovy
   nextflow_config:
     - manifest.name
     - manifest.homePage
@@ -25,3 +26,4 @@ lint:
     - lib/NfcoreTemplate.groovy
     - .prettierignore
   actions_ci: false
+  pipeline_name_conventions: false
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -157,7 +160,9 @@
                     "description": "Whether the samples should be converted to a gemini database"
                 }
             },
-            "required": ["scatter_size"]
+            "required": [
+                "scatter_size"
+            ]
         },
         "module_specific_parameters": {
             "title": "Module specific parameters",
@@ -292,7 +297,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -513,7 +525,8 @@
                 },
                 "vcfanno_lua": {
                     "type": "string",
-                    "default": "None"
+                    "default": "None",
+                    "description": "[Annotate & VCFanno mode only] The path to a Lua script to be used in VCFanno"
                 },
                 "vcfanno_resources": {
                     "type": "string",