Added nf-test for bedtools/jaccard (#6330)

modules/nf-core/bedtools/jaccard/tests/main.nf.test

@@ -0,0 +1,66 @@
+
+nextflow_process {
+
+    name "Test Process BEDTOOLS_JACCARD"
+    script "../main.nf"
+    process "BEDTOOLS_JACCARD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/jaccard"
+
+    test("test-bedtools-jaccard") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+				]
+				input[1] = [[],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-bedtools-jaccard-genome") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+				]
+				input[1] = [
+				    [ id:'genome' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-bedtools-jaccard-genome": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:08:36.70775"
+    },
+    "test-bedtools-jaccard": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:08:32.019101"
+    }
+}

modules/nf-core/bedtools/jaccard/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: "BEDTOOLS_JACCARD" {
+        ext.args = "-sorted"
+    }
+}

tests/config/pytest_modules.yml

@@ -67,9 +67,6 @@ beagle5/beagle:
 bedtools/intersect:
   - modules/nf-core/bedtools/intersect/**
   - tests/modules/nf-core/bedtools/intersect/**
-bedtools/jaccard:
-  - modules/nf-core/bedtools/jaccard/**
-  - tests/modules/nf-core/bedtools/jaccard/**
 bedtools/makewindows:
   - modules/nf-core/bedtools/makewindows/**
   - tests/modules/nf-core/bedtools/makewindows/**