From 7dee4476669957b3b53cd3e77dd7cdbc7b544a1a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:33:20 +0200
Subject: [PATCH] fix linting utils_nfschema_plugin

---
 .../nf-core/utils_nfschema_plugin/meta.yml    | 13 ++++
 .../utils_nfschema_plugin/tests/main.nf.test  | 63 +++++++++++++++++--
 2 files changed, 72 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index 90b8cb189..f7d9f0288 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -9,9 +9,22 @@ keywords:
   - summary
 components: []
 input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
   - validate_params:
       type: boolean
       description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
 output:
   - dummy_emit:
       type: boolean
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 703d3a9b8..842dc432a 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core subworkflows test utils_nfschema_plugin
 nextflow_workflow {
 
     name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
@@ -9,6 +7,7 @@ nextflow_workflow {
     tag "subworkflows"
     tag "subworkflows_nfcore"
     tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
 
     config "./nextflow.config"
 
@@ -23,7 +22,9 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = false
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
                 """
             }
         }
@@ -47,7 +48,61 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = true
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
                 """
             }
         }