From 1bb2e1eef9987588abf6759ce303a1435789ae21 Mon Sep 17 00:00:00 2001
From: KamilMaliszArdigen <kamil.malisz@ardigen.com>
Date: Thu, 31 Oct 2024 12:38:47 +0100
Subject: [PATCH] Tests update to cover new option

---
 .../limma/differential/tests/main.nf.test     |  4 +-
 .../differential/tests/main.nf.test.snap      | 47 ++++++++++++++-----
 .../tests/nextflow.voom_mixed.config          | 15 ++++++
 3 files changed, 52 insertions(+), 14 deletions(-)
 create mode 100644 modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config

diff --git a/modules/nf-core/limma/differential/tests/main.nf.test b/modules/nf-core/limma/differential/tests/main.nf.test
index 3a69cb5ed06..4cdd0014e71 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test
+++ b/modules/nf-core/limma/differential/tests/main.nf.test
@@ -277,8 +277,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.model, process.out.versions).match() },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.84055986312942") },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.705508451587681") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.8363444336503") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.736009837885068") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
             )
diff --git a/modules/nf-core/limma/differential/tests/main.nf.test.snap b/modules/nf-core/limma/differential/tests/main.nf.test.snap
index daa1489920b..8678f660a9f 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test.snap
+++ b/modules/nf-core/limma/differential/tests/main.nf.test.snap
@@ -17,10 +17,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:25:38.991424"
+        "timestamp": "2024-10-31T12:35:52.20676"
     },
     "test_limma_differential - voom": {
         "content": [
@@ -40,10 +40,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:26:07.303675"
+        "timestamp": "2024-10-31T12:36:19.251559"
     },
     "test_limma_differential - subset_to_contrast": {
         "content": [
@@ -63,10 +63,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:25:09.535356"
+        "timestamp": "2024-10-31T12:35:25.110644"
     },
     "test_limma_differential - exclude_samples": {
         "content": [
@@ -86,10 +86,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:24:15.276012"
+        "timestamp": "2024-10-31T12:34:25.24499"
     },
     "test_limma_differential - stub": {
         "content": [
@@ -133,10 +133,33 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:26:17.624889"
+        "timestamp": "2024-10-31T12:36:56.462834"
+    },
+    "test_limma_differential - voom_mixed": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "variable": "treatment",
+                        "reference": "hND6",
+                        "target": "mCherry"
+                    },
+                    "test.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6"
+                ]
+            ],
+            [
+                "versions.yml:md5,88a6e42d753077edab8daf829cd4d943"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T12:36:46.38894"
     },
     "test_limma_differential": {
         "content": [
@@ -156,9 +179,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:23:19.185283"
+        "timestamp": "2024-10-31T12:33:25.759977"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config
new file mode 100644
index 00000000000..95585efe13f
--- /dev/null
+++ b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config
@@ -0,0 +1,15 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'LIMMA_DIFFERENTIAL' {
+        ext.args = { [
+            "--sample_id_col sample",
+            "--probe_id_col gene_id",
+            "--use_voom TRUE",
+            "--mixed_model TRUE",
+            "--block sample_number"
+        ].join(' ').trim() }
+    }
+
+}