Clustering modules

.editorconfig

@@ -23,6 +23,9 @@ indent_size = unset
 [/assets/email*]
 indent_size = unset
 
+[/assets/ArborView.html]
+trim_trailing_whitespace = unset
+
 # ignore Readme
 [README.md]
 indent_style = unset

.gitignore

@@ -5,5 +5,7 @@ results/
 .DS_Store
 testing/
 testing*
+/.nf-test
+/.nf-test.log
 *.pyc
 *.swp

.nf-core.yml

@@ -22,6 +22,7 @@ lint:
     - assets/email_template.txt
     - docs/README.md
     - LICENSE
+    - .gitignore
   pipeline_name_conventions: False
   actions_awsfulltest: False
   multiqc_config:

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+/assets/ArborView.html

assets/schema_input.json

@@ -14,25 +14,13 @@
                 "unique": true,
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },
-            "fastq_1": {
+            "mlst_alleles": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
+                "format": "file-path",
+                "pattern": "^\\S+\\.mlst\\.json(\\.gz)?$",
+                "errorMessage": "MLST JSON file from locidex report, cannot contain spaces and must have the extension: '.mlst.json' or '.mlst.json.gz'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "mlst_alleles"]
     }
 }