Added nf-test for legsta

modules/nf-core/legsta/environment.yml

@@ -2,6 +2,5 @@ name: legsta
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::legsta=0.5.1

modules/nf-core/legsta/main.nf

@@ -30,4 +30,15 @@ process LEGSTA {
         legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;')
+    END_VERSIONS
+    """
 }

modules/nf-core/legsta/meta.yml

@@ -3,6 +3,8 @@ description: Typing of clinical and environmental isolates of Legionella pneumop
 keywords:
   - bacteria
   - legionella
+  - clinical
+  - pneumophila
 tools:
   - legsta:
       description: In silico Legionella pneumophila Sequence Based Typing

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

@@ -0,0 +1,57 @@
+
+nextflow_process {
+
+    name "Test Process LEGSTA"
+    script "../main.nf"
+    process "LEGSTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "legsta"
+
+    test("test-legsta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-legsta-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,72 @@
+{
+    "test-legsta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a853be87d21977365afe63ef07450a44"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a853be87d21977365afe63ef07450a44"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T20:09:21.017956"
+    },
+    "test-legsta-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a853be87d21977365afe63ef07450a44"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a853be87d21977365afe63ef07450a44"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T20:09:26.594828"
+    }
+}

tests/config/pytest_modules.yml

@@ -434,9 +434,6 @@ krona/ktupdatetaxonomy:
 leehom:
   - modules/nf-core/leehom/**
   - tests/modules/nf-core/leehom/**
-legsta:
-  - modules/nf-core/legsta/**
-  - tests/modules/nf-core/legsta/**
 limma/differential:
   - modules/nf-core/limma/differential/**
   - tests/modules/nf-core/limma/differential/**