add tests

subworkflows/local/utils_references/main.nf

@@ -1,3 +1,24 @@
+// JUST TO TEST THE SUBWORKFLOW
+
+workflow UTILS_REFERENCES {
+    take:
+    references
+    param_file
+    param_value
+    attribute_file
+    attribute_value
+    basepath
+
+    main:
+    // GIVING up writing a test for the functions, so writing a subworkflow to test it
+    references_file = extract_references_file(references, param_file, attribute_file, basepath)
+    references_value = extract_references_value(references, param_value, attribute_value)
+
+    emit:
+    references_file
+    references_value
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS TO EXTRACT REFERENCES FILES OR VALUES FROM THE REFERENCES YAML OR PARAMS
@@ -8,7 +29,7 @@ def extract_references_file(references, param, attribute, basepath) {
     return references
         .map { meta, _readme ->
             if (param || meta[attribute]) {
-                [meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', basepath))]
+                [meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', basepath), checkIfExists: true)]
             }
             else {
                 null

subworkflows/local/utils_references/meta.yml

@@ -0,0 +1,14 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_references"
+description: Functionality for dealing with references that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - references
+components: []
+input: []
+output: []
+authors:
+  - "@maxulysse"
+maintainers:
+  - "@maxulysse"

subworkflows/local/utils_references/tests/main.function.nf.test

@@ -0,0 +1,57 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+
+    test("extract_references_file - without params") {
+
+        function "extract_references_file"
+
+        when {
+            function {
+                """
+                input[0] = Channel.of([[
+                        genome:'GRCh38_chr22',
+                        id:'GRCh38_chr22',
+                        species:'Homo_sapiens',
+                        fasta:'\${params.igenomes_base}/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta',
+                    ], []])
+                input[1] = []
+                input[2] = 'fasta'
+                input[3] = 's3://nf-core-references/test_data/'
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+    }
+
+    test("extract_references_value - without params") {
+
+        function "extract_references_value"
+
+        when {
+            function {
+                """
+                input[0] = Channel.of([[
+                        genome:'GRCh38_chr22',
+                        id:'GRCh38_chr22',
+                        species:'Homo_sapiens',
+                        fasta:'\${params.igenomes_base}/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta',
+                    ], []])
+                input[1] = []
+                input[2] = 'species'
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+    }
+}

subworkflows/local/utils_references/tests/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_REFERENCES"
+    script "../main.nf"
+    workflow "UTILS_REFERENCES"
+
+    test("Without params") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([[
+                        genome:'GRCh38_chr22',
+                        id:'GRCh38_chr22',
+                        species:'Homo_sapiens',
+                        fasta:'\${params.igenomes_base}/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta',
+                    ], []])
+                input[1] = []
+                input[2] = []
+                input[3] = 'fasta'
+                input[4] = 'species'
+                input[5] = 's3://nf-core-references/test_data/'
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+    }
+
+    test("With params") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([[
+                        genome:'GRCh38_chr22',
+                        id:'GRCh38_chr22',
+                        species:'Homo_sapiens',
+                        fasta:'\${params.igenomes_base}/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta',
+                    ], []])
+                input[1] = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+                input[2] = 'WBCel235'
+                input[3] = 'fasta'
+                input[4] = 'species'
+                input[5] = 's3://nf-core-references/test_data/'
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+    }
+}

subworkflows/local/utils_references/tests/main.nf.test.snap

@@ -0,0 +1,88 @@
+{
+    "Without params": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "/nf-core-references/test_data/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "Homo_sapiens"
+                    ]
+                ],
+                "references_file": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "/nf-core-references/test_data/Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta"
+                    ]
+                ],
+                "references_value": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "Homo_sapiens"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-01-31T13:12:57.867733238"
+    },
+    "With params": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "WBCel235"
+                    ]
+                ],
+                "references_file": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
+                    ]
+                ],
+                "references_value": [
+                    [
+                        {
+                            "id": "GRCh38_chr22"
+                        },
+                        "WBCel235"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-01-31T13:13:08.097955852"
+    }
+}