Added nf-test for rtgtools/pedfilter (#6278)

* Added nf-test for rtgtools/pedfilter

* Updated power assertions

modules/nf-core/rtgtools/pedfilter/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.realtimegenomics.com/products/rtg-tools"
       documentation: "https://github.com/RealTimeGenomics/rtg-tools"
       tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map

modules/nf-core/rtgtools/pedfilter/tests/main.nf.test

@@ -0,0 +1,85 @@
+
+nextflow_process {
+
+    name "Test Process RTGTOOLS_PEDFILTER"
+    script "../main.nf"
+    process "RTGTOOLS_PEDFILTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rtgtools"
+    tag "rtgtools/pedfilter"
+
+    test("test-rtgtools-pedfilter-ped") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-rtgtools-pedfilter-vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-rtgtools-pedfilter-vcf-output") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.output[0][1]).linesGzip[3..7],
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+}

modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap

@@ -0,0 +1,91 @@
+{
+    "test-rtgtools-pedfilter-vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:11:01.797205"
+    },
+    "test-rtgtools-pedfilter-vcf-output": {
+        "content": [
+            [
+                "##CL=pedfilter --vcf justhusky.ped",
+                "##diseased=hugelymodelbat",
+                "##SAMPLE=<ID=earlycasualcaiman,Sex=MALE>",
+                "##SAMPLE=<ID=hugelymodelbat,Sex=MALE>",
+                "##SAMPLE=<ID=slowlycivilbuck,Sex=FEMALE>"
+            ],
+            [
+                "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T20:46:00.069224"
+    },
+    "test-rtgtools-pedfilter-ped": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:10:53.473351"
+    }
+}

modules/nf-core/rtgtools/pedfilter/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: 'RTGTOOLS_PEDFILTER' {
+        ext.args = "--vcf"
+    }
+}

tests/config/pytest_modules.yml

@@ -1241,9 +1241,6 @@ roary:
 rtgtools/format:
   - modules/nf-core/rtgtools/format/**
   - tests/modules/nf-core/rtgtools/format/**
-rtgtools/pedfilter:
-  - modules/nf-core/rtgtools/pedfilter/**
-  - tests/modules/nf-core/rtgtools/pedfilter/**
 rtgtools/vcfeval:
   - modules/nf-core/rtgtools/vcfeval/**
   - tests/modules/nf-core/rtgtools/vcfeval/**