Added nf-test for eido/validate (nf-core#6401)

* Added nf-test for eido/validate

* Fixed assertions

modules/nf-core/eido/validate/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: "http://eido.databio.org/en/latest/"
       documentation: "http://eido.databio.org/en/latest/"
       doi: "10.1093/gigascience/giab077"
-      licence: "BSD-2-Clause"
+      licence: ["BSD-2-Clause"]
 input:
   - samplesheet:
       type: file

modules/nf-core/eido/validate/tests/main.nf.test

@@ -0,0 +1,64 @@
+
+nextflow_process {
+
+    name "Test Process EIDO_VALIDATE"
+    script "../main.nf"
+    process "EIDO_VALIDATE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "eido"
+    tag "eido/validate"
+
+    test("test-eido-validate-on-nextflow-samplesheet") {
+
+        when {
+            process {
+                """
+                input[0] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
+				input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+				input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.log[0]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-eido-validate-on-pep-config") {
+
+        when {
+            process {
+                """
+                input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
+				input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+				input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.log[0]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/eido/validate/tests/main.nf.test.snap

@@ -0,0 +1,28 @@
+{
+    "test-eido-validate-on-pep-config": {
+        "content": [
+            "validation.log",
+            [
+                "versions.yml:md5,9a58d89818b4099d547bbaa9d2f2d8d9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-28T14:41:24.013292"
+    },
+    "test-eido-validate-on-nextflow-samplesheet": {
+        "content": [
+            "validation.log",
+            [
+                "versions.yml:md5,9a58d89818b4099d547bbaa9d2f2d8d9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-28T14:41:16.791933"
+    }
+}

modules/nf-core/eido/validate/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: 'EIDO_VALIDATE' {
+        ext.args = '--st-index sample'
+    }
+}

tests/config/pytest_modules.yml

@@ -247,9 +247,6 @@ ectyper:
 eido/convert:
   - modules/nf-core/eido/convert/**
   - tests/modules/nf-core/eido/convert/**
-eido/validate:
-  - modules/nf-core/eido/validate/**
-  - tests/modules/nf-core/eido/validate/**
 eigenstratdatabasetools/eigenstratsnpcoverage:
   - modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/**
   - tests/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/**