ltrharvest: Added test to verify graceful handling of no ltr input (#…

…5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic
nf-core · Jul 20, 2024 · 78575b0 · 78575b0
1 parent 4f1b730
commit 78575b0
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Showing 3 changed files with 66 additions and 36 deletions.
diff --git a/modules/nf-core/ltrharvest/tests/main.nf.test b/modules/nf-core/ltrharvest/tests/main.nf.test
@@ -8,14 +8,14 @@ nextflow_process {
     tag "modules_nfcore"
     tag "ltrharvest"
 
-    test("homo_sapiens-genome_21_fasta") {
+    test("homo_sapiens - genome_21_fasta") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -24,15 +24,45 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gff3).match("gff3") },
+                { assert snapshot(
+                    process.out.gff3,
+                    process.out.versions
+                    ).match()
+                },
                 { assert path(process.out.scn[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") },
-                { assert snapshot(path(process.out.versions[0]).text).match("script_versions") }
             )
         }
 
     }
 
-    test("homo_sapiens-genome_fasta-stub") {
+    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.gff3,
+                    process.out.versions
+                    ).match()
+                },
+                { assert path(process.out.scn[0][1]).text.contains("predictions are reported in the following way") },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - genome_fasta - stub") {
 
         options '-stub'
 
@@ -41,7 +71,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -50,8 +80,7 @@ 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/ltrharvest/tests/main.nf.test.snap b/modules/nf-core/ltrharvest/tests/main.nf.test.snap
@@ -1,5 +1,25 @@
 {
-    "homo_sapiens-genome_fasta-stub": {
+    "sarscov2 - genome_fasta - no_ltr": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gff3:md5,bddeb04277af08b5850e64708e8af02a"
+                ]
+            ],
+            [
+                "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:40:36.380052"
+    },
+    "homo_sapiens - genome_fasta - stub": {
         "content": [
             {
                 "0": [
@@ -44,21 +64,11 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-22T14:44:30.682167"
+        "timestamp": "2024-07-17T10:40:40.967557"
     },
-    "script_versions": {
-        "content": [
-            "\"LTRHARVEST\":\n    LTR_HARVEST_parallel: v1.1\n    genometools: 1.6.5\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-22T14:44:26.672478"
-    },
-    "gff3": {
+    "homo_sapiens - genome_21_fasta": {
         "content": [
             [
                 [
@@ -67,22 +77,15 @@
                     },
                     "test.gff3:md5,da13c4ba22e44ef944ddec38aa72c468"
                 ]
+            ],
+            [
+                "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-22T19:29:33.962761"
-    },
-    "stub_versions": {
-        "content": [
-            "\"LTRHARVEST\":\n    LTR_HARVEST_parallel: v1.1\n    genometools: 1.6.5\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-22T14:44:30.729166"
+        "timestamp": "2024-07-17T10:40:30.946"
     }
 }
diff --git a/modules/nf-core/ltrharvest/tests/tags.yml b/modules/nf-core/ltrharvest/tests/tags.yml