Merge pull request #2678 from mirpedrol/profile-comma

Template: add function to check `-profile` is well formatted

CHANGELOG.md

@@ -10,6 +10,7 @@
 - switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
 - Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 - Fix tyop in pipeline nextflow.config ([#2664](https://github.com/nf-core/tools/pull/2664))
+- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
 
 ### Download
 

nf_core/pipeline-template/lib/WorkflowMain.groovy

@@ -24,7 +24,7 @@ class WorkflowMain {
     //
     // Validate parameters and print summary to screen
     //
-    public static void initialise(workflow, params, log) {
+    public static void initialise(workflow, params, log, args) {
 
         // Print workflow version and exit on --version
         if (params.version) {
@@ -35,6 +35,8 @@ class WorkflowMain {
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
+        // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
+        checkProfile(workflow.profile, args, log)
 
         // Check that conda channels are set-up correctly
         if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -63,4 +65,16 @@ class WorkflowMain {
         return null
     }
     {%- endif %}
+
+    //
+    // Exit pipeline if --profile contains spaces
+    //
+    private static void checkProfile(profile, args, log) {
+        if (profile.endsWith(',')) {
+            Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
+        }
+        if (args[0]) {
+            log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n      Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
+        }
+    }
 }

nf_core/pipeline-template/main.nf

@@ -46,7 +46,7 @@ if (params.validate_params) {
     validateParameters()
 }
 
-WorkflowMain.initialise(workflow, params, log)
+WorkflowMain.initialise(workflow, params, log, args)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~