Added nf-test for gatk4/fastqtosam (#6315)

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

modules/nf-core/gatk4/fastqtosam/tests/main.nf.test

@@ -0,0 +1,64 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_FASTQTOSAM"
+    script "../main.nf"
+    process "GATK4_FASTQTOSAM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/fastqtosam"
+
+    test("test-gatk4-fastqtosam-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(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-gatk4-fastqtosam-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(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap

@@ -0,0 +1,28 @@
+{
+    "test-gatk4-fastqtosam-single-end": {
+        "content": [
+            "e6a4aa204d980e177a0458596f0a70ac",
+            [
+                "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:29:12.362942"
+    },
+    "test-gatk4-fastqtosam-paired-end": {
+        "content": [
+            "e6a4aa204d980e177a0458596f0a70ac",
+            [
+                "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:29:22.385798"
+    }
+}

tests/config/pytest_modules.yml

@@ -386,9 +386,6 @@ gatk4/createsomaticpanelofnormals:
 gatk4/determinegermlinecontigploidy:
   - modules/nf-core/gatk4/determinegermlinecontigploidy/**
   - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/**
-gatk4/fastqtosam:
-  - modules/nf-core/gatk4/fastqtosam/**
-  - tests/modules/nf-core/gatk4/fastqtosam/**
 gatk4/filtervarianttranches:
   - modules/nf-core/gatk4/filtervarianttranches/**
   - tests/modules/nf-core/gatk4/filtervarianttranches/**