Added nf-test for bbmap/clumpify (#6338)

* Added nf-test for bbmap/clumpify * Swap to snapshot all --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · d3b8821 · d3b8821
1 parent 2a6fda4
commit d3b8821
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diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test b/modules/nf-core/bbmap/clumpify/tests/main.nf.test
@@ -0,0 +1,72 @@
+
+nextflow_process {
+
+    name "Test Process BBMAP_CLUMPIFY"
+    script "../main.nf"
+    process "BBMAP_CLUMPIFY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/clumpify"
+
+    test("test-bbmap-clumpify-single-end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.reads,
+					file(process.out.log[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-bbmap-clumpify-paired-end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.reads,
+					file(process.out.log[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap
@@ -0,0 +1,49 @@
+{
+    "test-bbmap-clumpify-paired-end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c",
+                        "test_2.clumped.fastq.gz:md5,c70ab7bbd44d6b6fadd6a1a79ef1648f"
+                    ]
+                ]
+            ],
+            "test.clumpify.log",
+            [
+                "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T06:43:39.816170993"
+    },
+    "test-bbmap-clumpify-single-end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c"
+                ]
+            ],
+            "test.clumpify.log",
+            [
+                "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T06:43:28.923674245"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -55,9 +55,6 @@ bbmap/align:
 bbmap/bbnorm:
   - modules/nf-core/bbmap/bbnorm/**
   - tests/modules/nf-core/bbmap/bbnorm/**
-bbmap/clumpify:
-  - modules/nf-core/bbmap/clumpify/**
-  - tests/modules/nf-core/bbmap/clumpify/**
 bbmap/index:
   - modules/nf-core/bbmap/index/**
   - tests/modules/nf-core/bbmap/index/**

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