tests: update core tests for release candidate

Unchanged tests were run and did not change outcomes (as expected)

Author: J-81

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/tests/main.GLDS22.nf.test

@@ -0,0 +1,30 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "core"
+
+    test("GLDS-22: Should run without failures. First Test Case for Arabidopsis") {
+
+        when {
+            params {
+                // define parameters here. Example: 
+                osdAccession = "OSD-22"
+                gldsAccession = "GLDS-22"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                            path("${params.outputDir}/${params.gldsAccession}/Metadata").list(),
+                            path("${params.outputDir}/${params.gldsAccession}/00-RawData").list(),
+                            path("${params.outputDir}/${params.gldsAccession}/01-limma_NormExp").list(),
+                            path("${params.outputDir}/${params.gldsAccession}/02-limma_DGE").list(),
+                            path("${params.outputDir}/${params.gldsAccession}/GeneLab/software_versions.md")
+                            ).match()
+        }
+
+    }
+
+}

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/tests/main.GLDS22.nf.test.snap

@@ -0,0 +1,24 @@
+{
+    "GLDS-22: Should run without failures. First Test Case for Arabidopsis": {
+        "content": [
+            [
+                "OSD-22_metadata_OSD-22-ISA.zip:md5,54b9d89f37c99cc3b782ecb6b4f31c66",
+                "OSD-22_microarray_v0_runsheet.csv:md5,315cca3328a4fc58c0f2cb2862ec92e8"
+            ],
+            [
+                "raw_intensities.csv:md5,b796344835c59716d224f79d0a47abb6"
+            ],
+            [
+                "normalized_expression.csv:md5,031169ae9804ca0f97e0a5d530a40e88"
+            ],
+            [
+                "SampleTable.csv:md5,e06ec67d73d670aa67efaef842721895",
+                "contrasts.csv:md5,8d35c6eb5c8f554f902b26b782af9ecf",
+                "differential_expression.csv:md5,2c50db17385bef00f4f2c0a1a4b89606",
+                "visualization_PCA_table.csv:md5,588788b7b14c555ec34f1db88130cea1"
+            ],
+            "software_versions.md:md5,c39595e6b3b78288520518e77223b285"
+        ],
+        "timestamp": "2023-04-28T20:59:14+0000"
+    }
+}

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/tests/main.GLDS271.nf.test

@@ -23,7 +23,7 @@ nextflow_pipeline {
                             path("${params.outputDir}/${params.gldsAccession}/00-RawData").list(),
                             path("${params.outputDir}/${params.gldsAccession}/01-limma_NormExp").list(),
                             path("${params.outputDir}/${params.gldsAccession}/02-limma_DGE").list(),
-                            path("${params.outputDir}/${params.gldsAccession}/GeneLab").list()
+                            path("${params.outputDir}/${params.gldsAccession}/GeneLab/software_versions.md")
                             ).match()
         }
 

Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch/workflow_code/tests/main.GLDS271.nf.test.snap

@@ -17,11 +17,8 @@
                 "differential_expression.csv:md5,43b3bd3e169a3c0fb9fc8f7a70a2f7db",
                 "visualization_PCA_table.csv:md5,8185f12496c8467aa2affcfd0d982e62"
             ],
-            [
-                "NF_MAAgilent1ch_v1.0.1.html:md5,a26cc4ead0433796bf24e01a169e12fa",
-                "software_versions.md:md5,3611452371a61ccbbf8292fc6bbca357"
-            ]
+            "software_versions.md:md5,50a6ee7b99f0bb484286d08c1f7136e0"
         ],
-        "timestamp": "2023-04-27T22:57:19+0000"
+        "timestamp": "2023-04-28T21:02:43+0000"
     }
 }