Added nf-test for homer/annotatepeaks (#6573)

modules/nf-core/homer/annotatepeaks/main.nf

@@ -39,4 +39,16 @@ process HOMER_ANNOTATEPEAKS {
         homer: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.annotatePeaks.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
 }

modules/nf-core/homer/annotatepeaks/tests/main.nf.test

@@ -0,0 +1,68 @@
+
+nextflow_process {
+
+    name "Test Process HOMER_ANNOTATEPEAKS"
+    script "../main.nf"
+    process "HOMER_ANNOTATEPEAKS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "homer"
+    tag "homer/annotatepeaks"
+
+    test("test-homer-annotatepeaks") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.txt[0][1]).name, // unstable
+					process.out.stats,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-homer-annotatepeaks-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap

@@ -0,0 +1,62 @@
+{
+    "test-homer-annotatepeaks-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
+                ],
+                "stats": [
+
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:21:30.264399"
+    },
+    "test-homer-annotatepeaks": {
+        "content": [
+            "test.annotatePeaks.txt",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.annStats.txt:md5,eba336bce28fb5ec5d4ea3215b502dc5"
+                ]
+            ],
+            [
+                "versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:28:26.487711"
+    }
+}

modules/nf-core/homer/annotatepeaks/tests/nextflow.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = {"-annStats ${meta.id}.annStats.txt"}
+}

tests/config/pytest_modules.yml

@@ -359,9 +359,6 @@ hmmer/hmmbuild:
 hmtnote/annotate:
   - modules/nf-core/hmtnote/annotate/**
   - tests/modules/nf-core/hmtnote/annotate/**
-homer/annotatepeaks:
-  - modules/nf-core/homer/annotatepeaks/**
-  - tests/modules/nf-core/homer/annotatepeaks/**
 homer/makeucscfile:
   - modules/nf-core/homer/makeucscfile/**
   - tests/modules/nf-core/homer/makeucscfile/**