Added nf-test for gatk4/splitintervals (#6302)

* Added nf-test for gatk4/splitintervals * Added stub test
nf-core · Aug 27, 2024 · c335ccf · c335ccf
1 parent a8d18aa
commit c335ccf
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diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test
@@ -0,0 +1,109 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_SPLITINTERVALS"
+    script "../main.nf"
+    process "GATK4_SPLITINTERVALS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/splitintervals"
+
+    test("test-gatk4-splitintervals-bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+				]
+				input[1] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-gatk4-splitintervals-intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true)
+				]
+				input[1] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-gatk4-splitintervals-intervals-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true)
+				]
+				input[1] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = [ [ id:'genome' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap
@@ -0,0 +1,119 @@
+{
+    "test-gatk4-splitintervals-intervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,ebd6b34a335efc6732ff541936c6d2d5",
+                            "0001-scattered.interval_list:md5,9459b0e124fa84ec1e64ac4615bc9af7"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ],
+                "split_intervals": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,ebd6b34a335efc6732ff541936c6d2d5",
+                            "0001-scattered.interval_list:md5,9459b0e124fa84ec1e64ac4615bc9af7"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T11:06:41.633105"
+    },
+    "test-gatk4-splitintervals-bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,c8d6b19e7a92535b6ce9608eae558faa",
+                            "0001-scattered.interval_list:md5,b1877ad96aec308906594c50ebbe3ded"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ],
+                "split_intervals": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,c8d6b19e7a92535b6ce9608eae558faa",
+                            "0001-scattered.interval_list:md5,b1877ad96aec308906594c50ebbe3ded"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T11:06:28.504041"
+    },
+    "test-gatk4-splitintervals-intervals-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ],
+                "split_intervals": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-27T10:56:46.243594"
+    }
+}
diff --git a/modules/nf-core/gatk4/splitintervals/tests/nextflow.config b/modules/nf-core/gatk4/splitintervals/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_SPLITINTERVALS {
+        ext.args = "--scatter-count 2"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -398,9 +398,6 @@ gatk4/sitedepthtobaf:
 gatk4/splitcram:
   - modules/nf-core/gatk4/splitcram/**
   - tests/modules/nf-core/gatk4/splitcram/**
-gatk4/splitintervals:
-  - modules/nf-core/gatk4/splitintervals/**
-  - tests/modules/nf-core/gatk4/splitintervals/**
 gatk4/variantrecalibrator:
   - modules/nf-core/gatk4/variantrecalibrator/**
   - tests/modules/nf-core/gatk4/variantrecalibrator/**

diff --git a/tests/modules/nf-core/gatk4/splitintervals/main.nf b/tests/modules/nf-core/gatk4/splitintervals/main.nf
diff --git a/tests/modules/nf-core/gatk4/splitintervals/nextflow.config b/tests/modules/nf-core/gatk4/splitintervals/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/splitintervals/test.yml b/tests/modules/nf-core/gatk4/splitintervals/test.yml