Add automated linting fixer workflow

.devcontainer/devcontainer.json

@@ -1,14 +1,15 @@
 {
-  "image": "docker.io/nfcore/gitpod:2.9",
-  "features": {},
-  "customizations": {
-    "vscode": {
-      "extensions": [
-        "nextflow.nextflow",
-        "esbenp.prettier-vscode",
-        "redhat.vscode-yaml",
-        "GitHub.vscode-pull-request-github"
-      ]
+    "image": "docker.io/nfcore/gitpod:2.9",
+    "features": {},
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "nextflow.nextflow",
+                "esbenp.prettier-vscode",
+                "redhat.vscode-yaml",
+                "GitHub.vscode-pull-request-github",
+                "github.vscode-github-actions"
+            ]
+        }
     }
-  }
 }

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2

.prettierignore

@@ -1,9 +1,16 @@
 .nextflow*
+.editorconfig
+.gitignore
+.prettierignore
+LICENSE
 work/
-data/
 results/
 .DS_Store
-testing/
-testing*
+*.sh
 *.pyc
-bin/
+*.nf
+*.config
+*.test
+*.test.snap
+*.txt
+

nextflow_schema.json

@@ -1,38 +1,38 @@
 {
-  "$schema": "http://json-schema.org/draft-07/schema",
-  "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-  "title": ". pipeline parameters",
-  "description": "",
-  "type": "object",
-  "definitions": {
-    "parameters": {
-      "title": "Parameters",
-      "type": "object",
-      "description": "",
-      "default": "",
-      "properties": {
-        "skip": {
-          "type": "string",
-          "description": "Tests to skip as comma delimited values.",
-          "help_text": "Tests to skip as comma delimited values. E.g. --skip TEST_SUCCESS,TEST_INPUT. Case insensitive."
-        },
-        "remoteFile": {
-          "type": "string",
-          "description": "Path to remote file to download and use.",
-          "help_text": "Path to a remote file to use within the pipeline. This mimics a remote set of files such as reference data that may need to be retrieved prior to analysis. By default this is not specified and the test is not ran, add a remote file using standard Nextflow filenaming to pull a file from your storage (e.g. an S3 bucket or shared storage).",
-          "format": "path"
-        },
-        "outdir": {
-          "type": "string",
-          "description": "Path to use for publishing output files.",
-          "help_text": "Path to a remote folder to publish files to. If not specified, this is a subfolder within the working directory but if specified it will publish files to the path specified in this parameter."
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "parameters": {
+            "title": "Parameters",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "skip": {
+                    "type": "string",
+                    "description": "Tests to skip as comma delimited values.",
+                    "help_text": "Tests to skip as comma delimited values. E.g. --skip TEST_SUCCESS,TEST_INPUT. Case insensitive."
+                },
+                "remoteFile": {
+                    "type": "string",
+                    "description": "Path to remote file to download and use.",
+                    "help_text": "Path to a remote file to use within the pipeline. This mimics a remote set of files such as reference data that may need to be retrieved prior to analysis. By default this is not specified and the test is not ran, add a remote file using standard Nextflow filenaming to pull a file from your storage (e.g. an S3 bucket or shared storage).",
+                    "format": "path"
+                },
+                "outdir": {
+                    "type": "string",
+                    "description": "Path to use for publishing output files.",
+                    "help_text": "Path to a remote folder to publish files to. If not specified, this is a subfolder within the working directory but if specified it will publish files to the path specified in this parameter."
+                }
+            }
         }
-      }
-    }
-  },
-  "allOf": [
-    {
-      "$ref": "#/definitions/parameters"
-    }
-  ]
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/parameters"
+        }
+    ]
 }