add checkProfileProvided to utils_nfcore_pipeline

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 },