Added nf-test for goat/taxonsearch

modules/nf-core/goat/taxonsearch/main.nf

@@ -33,4 +33,19 @@ process GOAT_TAXONSEARCH {
         goat: \$(goat-cli --version | cut -d' ' -f2)
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    input = taxa_file ? "-f ${taxa_file}" : "-t \"${taxon}\""
+    if (!taxon && !taxa_file) error "No input. Valid input: single taxon identifier or a .txt file with identifiers"
+    if (taxon && taxa_file ) error "Only one input is required: a single taxon identifier or a .txt file with identifiers"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        goat: \$(goat-cli --version | cut -d' ' -f2)
+    END_VERSIONS
+    """
 }

modules/nf-core/goat/taxonsearch/tests/main.nf.test

@@ -0,0 +1,107 @@
+
+nextflow_process {
+
+    name "Test Process GOAT_TAXONSEARCH"
+    script "../main.nf"
+    process "GOAT_TAXONSEARCH"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "goat"
+    tag "goat/taxonsearch"
+
+    test("test-goat-taxonsearch-single-species") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test_single_species' ], // meta map
+				    'Meles meles',
+				    []
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-goat-taxonsearch-genus-id") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test_genus_id' ], // meta map
+				    '7215',
+				    []
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-goat-taxonsearch-species") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test_species' ], // meta map
+				    '',
+				    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/generic/txt/species_names.txt', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-goat-taxonsearch-species-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test_species' ], // meta map
+				    '',
+				    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/generic/txt/species_names.txt', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/goat/taxonsearch/tests/main.nf.test.snap

@@ -0,0 +1,134 @@
+{
+    "test-goat-taxonsearch-species": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_species"
+                        },
+                        "test_species.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ],
+                "taxonsearch": [
+                    [
+                        {
+                            "id": "test_species"
+                        },
+                        "test_species.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:10:06.012895"
+    },
+    "test-goat-taxonsearch-species-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_species"
+                        },
+                        "test_species.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ],
+                "taxonsearch": [
+                    [
+                        {
+                            "id": "test_species"
+                        },
+                        "test_species.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:10:10.398213"
+    },
+    "test-goat-taxonsearch-genus-id": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_genus_id"
+                        },
+                        "test_genus_id.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ],
+                "taxonsearch": [
+                    [
+                        {
+                            "id": "test_genus_id"
+                        },
+                        "test_genus_id.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:09:58.101426"
+    },
+    "test-goat-taxonsearch-single-species": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_single_species"
+                        },
+                        "test_single_species.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ],
+                "taxonsearch": [
+                    [
+                        {
+                            "id": "test_single_species"
+                        },
+                        "test_single_species.tsv:md5,31d1bc139e5e507015e2ab0581708633"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d07de5ffeab892f448b03802528bfbbb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:09:51.117911"
+    }
+}

modules/nf-core/goat/taxonsearch/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: GOAT_TAXONSEARCH {
+         ext.args = '-l -b'
+     }
+}

tests/config/pytest_modules.yml

@@ -320,9 +320,6 @@ glimpse2/concordance:
 glnexus:
   - modules/nf-core/glnexus/**
   - tests/modules/nf-core/glnexus/**
-goat/taxonsearch:
-  - modules/nf-core/goat/taxonsearch/**
-  - tests/modules/nf-core/goat/taxonsearch/**
 goleft/indexsplit:
   - modules/nf-core/goleft/indexsplit/**
   - tests/modules/nf-core/goleft/indexsplit/**