test updio and merge_beds

nf-cmgg · Nov 14, 2024 · 4f200f1 · 4f200f1
1 parent b896143
commit 4f200f1
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diff --git a/modules/local/merge_beds/tests/main.nf.test b/modules/local/merge_beds/tests/main.nf.test
@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process MERGE_BEDS"
+    script "../main.nf"
+    process "MERGE_BEDS"
+
+    tag "modules"
+    tag "modules_local"
+    tag "merge_beds"
+
+    test("homo_sapiens - bed") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.bed, checkIfExists:true)
+                ]
+                input[1] = [
+                    [ id:'fai' ],
+                    file(params.fai, checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bed - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.bed, checkIfExists:true)
+                ]
+                input[1] = [
+                    [ id:'fai' ],
+                    file(params.fai, checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/merge_beds/tests/main.nf.test.snap b/modules/local/merge_beds/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "homo_sapiens - bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,fa245abf8add7a80650566a1de67ec04"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,273f887b675fb5feb6073a5313a191a9"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,fa245abf8add7a80650566a1de67ec04"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,273f887b675fb5feb6073a5313a191a9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:49:08.980488978"
+    },
+    "homo_sapiens - bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,273f887b675fb5feb6073a5313a191a9"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,273f887b675fb5feb6073a5313a191a9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:49:17.089675797"
+    }
+}
diff --git a/modules/local/merge_beds/tests/nextflow.config b/modules/local/merge_beds/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-d 150"
+}
diff --git a/modules/local/updio/tests/main.nf.test b/modules/local/updio/tests/main.nf.test
@@ -0,0 +1,63 @@
+nextflow_process {
+
+    name "Test Process UPDIO"
+    script "../main.nf"
+    process "UPDIO"
+
+    tag "modules"
+    tag "modules_local"
+    tag "updio"
+
+    test("homo_sapiens - vcf, tbi, []") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', child:'NA24385' ], // meta map
+                    file(params.famvcf, checkIfExists:true),
+                    file(params.famtbi, checkIfExists:true)
+                ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf, tbi, [] - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', child:'NA24385' ], // meta map
+                    file(params.famvcf, checkIfExists:true),
+                    file(params.famtbi, checkIfExists:true)
+                ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/local/updio/tests/main.nf.test.snap b/modules/local/updio/tests/main.nf.test.snap
@@ -0,0 +1,92 @@
+{
+    "homo_sapiens - vcf, tbi, [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "child": "NA24385"
+                        },
+                        [
+                            "NA24385.events_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.table:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.upd:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8a807f51c31f64de1c707210fabe7029"
+                ],
+                "updio": [
+                    [
+                        {
+                            "id": "test",
+                            "child": "NA24385"
+                        },
+                        [
+                            "NA24385.events_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.table:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "NA24385.upd:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8a807f51c31f64de1c707210fabe7029"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:57:26.032830013"
+    },
+    "homo_sapiens - vcf, tbi, []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "child": "NA24385"
+                        },
+                        [
+                            "NA24385.events_list:md5,4a26c133ef193d31eddfd18dae94f0a0",
+                            "NA24385.log:md5,a40a24f379127a9cde7e40a1ce1032ec",
+                            "NA24385.table:md5,ca8165fc7869a113ca034396de7cf579",
+                            "NA24385.upd:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8a807f51c31f64de1c707210fabe7029"
+                ],
+                "updio": [
+                    [
+                        {
+                            "id": "test",
+                            "child": "NA24385"
+                        },
+                        [
+                            "NA24385.events_list:md5,4a26c133ef193d31eddfd18dae94f0a0",
+                            "NA24385.log:md5,a40a24f379127a9cde7e40a1ce1032ec",
+                            "NA24385.table:md5,ca8165fc7869a113ca034396de7cf579",
+                            "NA24385.upd:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8a807f51c31f64de1c707210fabe7029"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:57:17.522197249"
+    }
+}
diff --git a/modules/local/updio/tests/nextflow.config b/modules/local/updio/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "--childID NA24385 --momID NA24149 --dadID NA24143"
+}