Added nf-test for picard/fastqtosam (#6295)

modules/nf-core/picard/fastqtosam/tests/main.nf.test

@@ -0,0 +1,100 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_FASTQTOSAM"
+    script "../main.nf"
+    process "PICARD_FASTQTOSAM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/fastqtosam"
+
+    test("test-picard-fastqtosam-single") {
+
+        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(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-picard-fastqtosam-paired") {
+
+        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(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-picard-fastqtosam-paired-custom-samplename") {
+        config "./nextflow.config"
+
+        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(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap

@@ -0,0 +1,41 @@
+{
+    "test-picard-fastqtosam-paired-custom-samplename": {
+        "content": [
+            "e3cfa46b13cc4fc425cccae944f43b10",
+            [
+                "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:50:01.762254"
+    },
+    "test-picard-fastqtosam-single": {
+        "content": [
+            "e6a4aa204d980e177a0458596f0a70ac",
+            [
+                "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:49:32.460549"
+    },
+    "test-picard-fastqtosam-paired": {
+        "content": [
+            "e3cfa46b13cc4fc425cccae944f43b10",
+            [
+                "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:49:47.018269"
+    }
+}

modules/nf-core/picard/fastqtosam/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: 'PICARD_FASTQTOSAM' {
+        ext.args = "--SAMPLE_NAME CustomSample"
+    }
+}

tests/config/pytest_modules.yml

@@ -935,9 +935,6 @@ picard/collectinsertsizemetrics:
 picard/collectrnaseqmetrics:
   - modules/nf-core/picard/collectrnaseqmetrics/**
   - tests/modules/nf-core/picard/collectrnaseqmetrics/**
-picard/fastqtosam:
-  - modules/nf-core/picard/fastqtosam/**
-  - tests/modules/nf-core/picard/fastqtosam/**
 picard/filtersamreads:
   - modules/nf-core/picard/filtersamreads/**
   - tests/modules/nf-core/picard/filtersamreads/**