Added nf-test for blat (#6603)

Co-authored-by: Simon Pearce <[email protected]>

modules/nf-core/blat/tests/main.nf.test

@@ -0,0 +1,75 @@
+
+nextflow_process {
+
+    name "Test Process BLAT"
+    script "../main.nf"
+    process "BLAT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "blat"
+    tag "seqtk/seq"
+
+    setup {
+        run("SEQTK_SEQ") {
+            script "../../seqtk/seq/main.nf"
+            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)
+				]
+
+                """
+            }
+        }
+    }
+
+    test("test-blat") {
+
+        when {
+            process {
+                """
+                input[0] = SEQTK_SEQ.out.fastx
+				input[1] = [
+				    [ id:'sarscov2' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-blat-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = SEQTK_SEQ.out.fastx
+				input[1] = [
+				    [ id:'sarscov2' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/blat/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-blat": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ],
+                "psl": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T20:38:03.56409"
+    },
+    "test-blat-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ],
+                "psl": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T20:38:09.736595"
+    }
+}

modules/nf-core/blat/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: SEQTK_SEQ {
+        ext.args = '-A'
+    }
+}

tests/config/pytest_modules.yml

@@ -52,9 +52,6 @@ bedtools/unionbedg:
 biohansel:
   - modules/nf-core/biohansel/**
   - tests/modules/nf-core/biohansel/**
-blat:
-  - modules/nf-core/blat/**
-  - tests/modules/nf-core/blat/**
 cadd:
   - modules/nf-core/cadd/**
   - tests/modules/nf-core/cadd/**