Added nf-test for mmseqs/databases

modules/nf-core/mmseqs/createtsv/environment.yml

@@ -2,6 +2,5 @@ name: mmseqs_createtsv
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::mmseqs2=15.6f452

modules/nf-core/mmseqs/databases/environment.yml

@@ -2,6 +2,5 @@ name: mmseqs_databases
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::mmseqs2=15.6f452

modules/nf-core/mmseqs/databases/main.nf

@@ -11,8 +11,8 @@ process MMSEQS_DATABASES {
     val database
 
     output:
-    path "${prefix}/" , emit: database
-    path "versions.yml"     , emit: versions
+    path "${prefix}/"   , emit: database
+    path "versions.yml" , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/mmseqs/databases/tests/main.nf.test

@@ -0,0 +1,55 @@
+
+nextflow_process {
+
+    name "Test Process MMSEQS_DATABASES"
+    script "../main.nf"
+    process "MMSEQS_DATABASES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/databases"
+
+    test("test-mmseqs-databases") {
+
+        when {
+            process {
+                """
+                input[0] = "SILVA"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.database[0]).listFiles().collect { it.name }.toSorted(), // unstable
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-mmseqs-databases-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = "SILVA"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/mmseqs/databases/tests/main.nf.test.snap

@@ -0,0 +1,74 @@
+{
+    "test-mmseqs-databases": {
+        "content": [
+            [
+                "database",
+                "database.dbtype",
+                "database.index",
+                "database.lookup",
+                "database.source",
+                "database.version",
+                "database_h",
+                "database_h.dbtype",
+                "database_h.index",
+                "database_mapping",
+                "database_taxonomy"
+            ],
+            [
+                "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T15:43:58.454012"
+    },
+    "test-mmseqs-databases-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "database:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.version:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3"
+                ],
+                "database": [
+                    [
+                        "database:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.version:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T17:00:20.527628"
+    }
+}

modules/nf-core/mmseqs/taxonomy/environment.yml

@@ -4,6 +4,5 @@ name: "mmseqs_taxonomy"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::mmseqs2=15.6f452"

tests/config/pytest_modules.yml

@@ -473,9 +473,6 @@ mitohifi/mitohifi:
 mmseqs/cluster:
   - modules/nf-core/mmseqs/cluster/**
   - tests/modules/nf-core/mmseqs/cluster/**
-mmseqs/databases:
-  - modules/nf-core/mmseqs/databases/**
-  - tests/modules/nf-core/mmseqs/databases/**
 mmseqs/easysearch:
   - modules/nf-core/mmseqs/easysearch/**
   - tests/modules/nf-core/mmseqs/easysearch/**