Added nf-test for samtools/depth (nf-core#6275)

modules/nf-core/samtools/depth/environment.yml

@@ -1,8 +1,10 @@
 name: samtools_depth
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::samtools=1.20
   - bioconda::htslib=1.20
+  - bioconda::samtools=1.20

modules/nf-core/samtools/depth/tests/main.nf.test

@@ -0,0 +1,62 @@
+
+nextflow_process {
+
+    name "Test Process SAMTOOLS_DEPTH"
+    script "../main.nf"
+    process "SAMTOOLS_DEPTH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/depth"
+
+    test("test-samtools-depth") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true)
+                ]
+				input[1] = [[],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-samtools-depth-intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true)
+                ]
+				input[1] = [
+                    [ id:'bed' ],
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/samtools/depth/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-samtools-depth-intervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,a89e2f8e1b66356c7500599fcadb8784"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,a89e2f8e1b66356c7500599fcadb8784"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:57:20.065271"
+    },
+    "test-samtools-depth": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,722d2c060944d6b96ae5ae00d8074657"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,722d2c060944d6b96ae5ae00d8074657"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:57:13.724175"
+    }
+}

tests/config/pytest_modules.yml

@@ -1268,9 +1268,6 @@ sambamba/markdup:
 samtools/collatefastq:
   - modules/nf-core/samtools/collatefastq/**
   - tests/modules/nf-core/samtools/collatefastq/**
-samtools/depth:
-  - modules/nf-core/samtools/depth/**
-  - tests/modules/nf-core/samtools/depth/**
 samtools/fasta:
   - modules/nf-core/samtools/fasta/**
   - tests/modules/nf-core/samtools/fasta/**