add checkProfileProvided to utils_nfcore_pipeline (#4891)

subworkflows/nf-core/utils_nfcore_pipeline/main.nf

@@ -13,8 +13,12 @@ import nextflow.extension.FilesEx
 
 workflow UTILS_NFCORE_PIPELINE {
 
+    take:
+    nextflow_cli_args
+
     main:
     valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
 
     emit:
     valid_config
@@ -43,6 +47,20 @@ def checkConfigProvided() {
     return valid_config
 }
 
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+    if (workflow.profile.endsWith(',')) {
+        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+    if (nextflow_cli_args[0]) {
+        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+}
+
 //
 // Citation string for pipeline
 //

subworkflows/nf-core/utils_nfcore_pipeline/meta.yml

@@ -7,7 +7,11 @@ keywords:
   - initialise
   - version
 components: []
-input: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
 output:
   - success:
       type: boolean

subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test

@@ -21,6 +21,26 @@ nextflow_function {
         }
     }
 
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
     test("Test Function workflowCitation") {
 
         function "workflowCitation"

subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test

@@ -11,6 +11,14 @@ nextflow_workflow {
 
     test("Should run without failures") {
 
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert workflow.success },