added basicpy nftest

.github/conda_skip.yml

@@ -16,6 +16,8 @@ exclude:
     path: modules/nf-core/bakta/baktadbdownload
   - profile: conda
     path: modules/nf-core/bases2fastq
+  - profile: conda
+    path: modules/nf-core/basicpy
   - profile: conda
     path: modules/nf-core/bcl2fastq
   - profile: conda
@@ -184,7 +186,7 @@ exclude:
     path: modules/nf-core/xeniumranger/import-segmentation
   - profile: conda
     path: modules/nf-core/parabricks/mutectcaller
- - profile: conda
+  - profile: conda
     path: modules/nf-core/parabricks/dbsnp
   - profile: conda
     path: modules/nf-core/parabricks/indexgvcf

modules/nf-core/basicpy/main.nf

@@ -19,15 +19,15 @@ process BASICPY {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args    = task.ext.args   ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.2.0-patch1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
     """
     /opt/main.py -i $image -o . $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        basicpy:: $VERSION
+        basicpy: $VERSION
     END_VERSIONS
     """
 
@@ -36,13 +36,15 @@ process BASICPY {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
     }
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "1.2.0-patch1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
     """
     touch ${prefix}.-dfp.tiff
     touch ${prefix}.-dfp.tiff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        basicpy:: $VERSION
+        basicpy: $VERSION
     END_VERSIONS
     """
 }

modules/nf-core/basicpy/tests/main.nf.test

@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process BASICPY"
+    script "../main.nf"
+    process "BASICPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "basicpy"
+
+    test("basicpy - OME-TIFF") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("basicpy - OME-TIFF - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/basicpy/tests/main.nf.test.snap

@@ -0,0 +1,74 @@
+{
+    "basicpy - OME-TIFF": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "cycif-tonsil-cycle1.ome-dfp.tiff:md5,ed8e02bbd04d694ff5a5f289f48f97ab",
+                            "cycif-tonsil-cycle1.ome-ffp.tiff:md5,e1a1a2398ef5b76110db6114541f7511"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1391fd5a5745a20016f9824467273113"
+                ],
+                "fields": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "cycif-tonsil-cycle1.ome-dfp.tiff:md5,ed8e02bbd04d694ff5a5f289f48f97ab",
+                            "cycif-tonsil-cycle1.ome-ffp.tiff:md5,e1a1a2398ef5b76110db6114541f7511"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1391fd5a5745a20016f9824467273113"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-16T10:57:29.262528119"
+    },
+    "basicpy - OME-TIFF - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1391fd5a5745a20016f9824467273113"
+                ],
+                "fields": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1391fd5a5745a20016f9824467273113"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-16T10:57:35.685056461"
+    }
+}

tests/config/pytest_modules.yml

@@ -37,9 +37,6 @@ bamtools/convert:
 bamtools/split:
   - modules/nf-core/bamtools/split/**
   - tests/modules/nf-core/bamtools/split/**
-basicpy:
-  - modules/nf-core/basicpy/**
-  - tests/modules/nf-core/basicpy/**
 bbmap/align:
   - modules/nf-core/bbmap/align/**
   - tests/modules/nf-core/bbmap/align/**