biscuit/align nf-test and snapshot

modules/nf-core/biscuit/align/tests/main.nf.test

@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process BISCUIT_ALIGN"
+    script "../main.nf"
+    process "BISCUIT_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "biscuit"
+    tag "biscuit/align"
+    tag "biscuit/index"
+
+    setup {
+        run("BISCUIT_INDEX") {
+            script "../../index/main.nf"
+            process {
+            """
+            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            """
+        }
+        }
+    }
+
+    test("Single-End sarscov2 test_methylated_1 [fastq_gz]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+                ]
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.bam[0][1]).name == "test.bam" },
+                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
+                { assert snapshot(process.out.versions).match("single-end-versions") }
+          )
+        }
+    }
+
+    test("Paired-End sarscov2 test_methylated_1 [fastq_gz]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                              file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+                ]
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.bam[0][1]).name == "test.bam" },
+                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
+                { assert snapshot(process.out.versions).match("paired-end-versions") }
+          )
+        }
+    }
+}

modules/nf-core/biscuit/align/tests/main.nf.test.snap

@@ -0,0 +1,26 @@
+{
+    "single-end-versions": {
+        "content": [
+            [
+                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T20:06:02.295706212"
+    },
+    "paired-end-versions": {
+        "content": [
+            [
+                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T20:06:17.879689395"
+    }
+}

modules/nf-core/biscuit/align/tests/tags.yml

@@ -0,0 +1,3 @@
+biscuit/align:
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/align/**

tests/config/pytest_modules.yml

@@ -184,10 +184,6 @@ biobambam/bamsormadup:
 biohansel:
   - modules/nf-core/biohansel/**
   - tests/modules/nf-core/biohansel/**
-biscuit/align:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/align/**
-  - tests/modules/nf-core/biscuit/align/**
 biscuit/biscuitblaster:
   - modules/nf-core/biscuit/index/**
   - modules/nf-core/biscuit/biscuitblaster/**