nf-test for snpsites

modules/nf-core/snpsites/tests/main.nf.test

@@ -0,0 +1,29 @@
+nextflow_process {
+
+    name "Test Process SNPSITES"
+    script "../main.nf"
+    process "SNPSITES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "snpsites"
+
+    test("sarscov2 - all_sites_fas") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}

modules/nf-core/snpsites/tests/main.nf.test.snap

@@ -0,0 +1,50 @@
+{
+    "constant_sites": {
+        "content": [
+            [
+                "constant.sites.txt:md5,8b9b226e3787f7baaefce07405af22c9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T16:10:41.912047"
+    },
+    "Test snpsites": {
+        "content": [
+            [
+                "versions.yml:md5,af6942a02036a7ff2eadb6ecf344c619"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T15:59:15.769873"
+    },
+    "constant_sites_string": {
+        "content": [
+            [
+                "8789,5363,5747,9456"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T15:59:15.817838"
+    },
+    "fasta": {
+        "content": [
+            [
+                "filtered_alignment.fas:md5,f96c7513003e878e16fa9eac9fcda0f4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T15:59:15.823904"
+    }
+}

modules/nf-core/snpsites/tests/tags.yml

@@ -0,0 +1,2 @@
+snpsites:
+  - "modules/nf-core/snpsites/**"

tests/config/pytest_modules.yml

@@ -1877,9 +1877,6 @@ snpsift/dbnsfp:
 snpsift/split:
   - modules/nf-core/snpsift/split/**
   - tests/modules/nf-core/snpsift/split/**
-snpsites:
-  - modules/nf-core/snpsites/**
-  - tests/modules/nf-core/snpsites/**
 somalier/ancestry:
   - modules/nf-core/somalier/ancestry/**
   - tests/modules/nf-core/somalier/ancestry/**