From be4f907729fce59ca73b6d79545cd220544729c7 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Sat, 20 Jul 2024 12:39:09 +1200
Subject: [PATCH] ltrfinder: Added test to verify graceful handling of no ltr
 input (#5979)

---
 modules/nf-core/ltrfinder/tests/main.nf.test  | 32 +++++++++--
 .../nf-core/ltrfinder/tests/main.nf.test.snap | 57 ++++++++++++++-----
 modules/nf-core/ltrfinder/tests/tags.yml      |  2 -
 3 files changed, 69 insertions(+), 22 deletions(-)
 delete mode 100644 modules/nf-core/ltrfinder/tests/tags.yml

diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test
index 447ce34d3e1..f971f7bb1f7 100644
--- a/modules/nf-core/ltrfinder/tests/main.nf.test
+++ b/modules/nf-core/ltrfinder/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true)
                     ]
                     """
                 }
@@ -37,8 +37,29 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(path(process.out.versions[0]).text).match("versions") }
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2-genome_fasta-no_ltr") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -53,7 +74,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -62,8 +83,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(path(process.out.versions[0]).text).match("stub_versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test.snap b/modules/nf-core/ltrfinder/tests/main.nf.test.snap
index 54a2cee10f2..0f1790fc6fe 100644
--- a/modules/nf-core/ltrfinder/tests/main.nf.test.snap
+++ b/modules/nf-core/ltrfinder/tests/main.nf.test.snap
@@ -48,15 +48,54 @@
         },
         "timestamp": "2024-02-16T09:14:38.509965"
     },
-    "versions": {
+    "sarscov2-genome_fasta-no_ltr": {
         "content": [
-            "\"LTRFINDER\":\n    LTR_FINDER_parallel: v1.1\n    ltr_finder: v1.07\n"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scn:md5,2ce449dff751e59dbc292b6888491954"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,bddeb04277af08b5850e64708e8af02a"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7b24225b810fa88cfb2a887de11be333"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,bddeb04277af08b5850e64708e8af02a"
+                    ]
+                ],
+                "scn": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scn:md5,2ce449dff751e59dbc292b6888491954"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7b24225b810fa88cfb2a887de11be333"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-16T09:16:55.301422"
+        "timestamp": "2024-07-16T13:03:03.505263"
     },
     "stub": {
         "content": [
@@ -106,15 +145,5 @@
             "nextflow": "23.10.1"
         },
         "timestamp": "2024-02-16T09:14:43.054758"
-    },
-    "stub_versions": {
-        "content": [
-            "\"LTRFINDER\":\n    LTR_FINDER_parallel: v1.1\n    ltr_finder: v1.07\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-16T09:16:59.800724"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ltrfinder/tests/tags.yml b/modules/nf-core/ltrfinder/tests/tags.yml
deleted file mode 100644
index 006ded2c8ff..00000000000
--- a/modules/nf-core/ltrfinder/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-ltrfinder:
-  - "modules/nf-core/ltrfinder/**"