From 7f0f5c74c4bd09278b9d04dc628b577fa5f485b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Fri, 9 Feb 2024 19:57:14 +0100
Subject: [PATCH] add checkProfileProvided to utils_nfcore_pipeline (#4891)

---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 18 +++++++++++++++++
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  6 +++++-
 .../tests/main.function.nf.test               | 20 +++++++++++++++++++
 .../tests/main.function.nf.test.snap          |  4 ++++
 .../tests/main.workflow.nf.test               |  8 ++++++++
 5 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 6d805bb3fda7..c1aecf6e42b1 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/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
 //
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
index dd1462b23225..d08d24342d88 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
+++ b/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
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index f7ea05fcd7f2..1dc317f8f7b4 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/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"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index afb9ab4dca2b..10f948e629cc 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,4 +1,8 @@
 {
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "timestamp": "2024-02-09T15:43:55.145717"
+    },
     "Test Function checkConfigProvided": {
         "content": [
             true
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index c5f7776a6715..8940d32d1efb 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/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 },