Added nf-test for gatk4/gatherbqsrreports

nf-core · Aug 26, 2024 · d7335a8 · d7335a8
1 parent 13b1571
commit d7335a8
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Showing 6 changed files with 132 additions and 54 deletions.
diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test
@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_GATHERBQSRREPORTS"
+    script "../main.nf"
+    process "GATK4_GATHERBQSRREPORTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/gatherbqsrreports"
+
+    test("test-gatk4-gatherbqsrreports") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-gatk4-gatherbqsrreports-multiple") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table', checkIfExists: true)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test-gatk4-gatherbqsrreports-multiple": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.table:md5,0c1257eececf95db8ca378272d0f21f9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.table:md5,0c1257eececf95db8ca378272d0f21f9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:22:34.490694"
+    },
+    "test-gatk4-gatherbqsrreports": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:22:10.552951"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -473,9 +473,6 @@ gatk4/filterintervals:
 gatk4/filtervarianttranches:
   - modules/nf-core/gatk4/filtervarianttranches/**
   - tests/modules/nf-core/gatk4/filtervarianttranches/**
-gatk4/gatherbqsrreports:
-  - modules/nf-core/gatk4/gatherbqsrreports/**
-  - tests/modules/nf-core/gatk4/gatherbqsrreports/**
 gatk4/gatherpileupsummaries:
   - modules/nf-core/gatk4/gatherpileupsummaries/**
   - tests/modules/nf-core/gatk4/gatherpileupsummaries/**

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