Added nf-test for geoquery/getgeo

modules/nf-core/geoquery/getgeo/environment.yml

@@ -2,6 +2,5 @@ name: geoquery_getgeo
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bioconductor-geoquery=2.66.0

modules/nf-core/geoquery/getgeo/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html"
       tool_dev_url: "https://github.com/seandavi/GEOquery"
       doi: "10.1093/bioinformatics/btm254"
-      licence: "MIT"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/nf-core/geoquery/getgeo/tests/main.nf.test

@@ -0,0 +1,70 @@
+
+nextflow_process {
+
+    name "Test Process GEOQUERY_GETGEO"
+    script "../main.nf"
+    process "GEOQUERY_GETGEO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "geoquery"
+    tag "geoquery/getgeo"
+
+    test("test-geoquery-getgeo") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    'GSE50790'
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.rds[0][1]).name,
+					process.out.expression,
+					process.out.annotation,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-geoquery-getgeo-with-metacols") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    'GSE50790'
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.rds[0][1]).name,
+					process.out.expression,
+					process.out.annotation,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap

@@ -0,0 +1,60 @@
+{
+    "test-geoquery-getgeo-with-metacols": {
+        "content": [
+            "test.eset.rds",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.matrix.tsv:md5,230f87f91c0c1a7e2ab354200c4b978c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.annotation.tsv:md5,40300ae222ae35fa54daf10a1b86e830"
+                ]
+            ],
+            [
+                "versions.yml:md5,975445af2def0ea44ea949ff5aee1fc0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T08:37:33.606465"
+    },
+    "test-geoquery-getgeo": {
+        "content": [
+            "eset.rds",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "matrix.tsv:md5,230f87f91c0c1a7e2ab354200c4b978c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "annotation.tsv:md5,4dbb874b49a11dff13557f58da643ee0"
+                ]
+            ],
+            [
+                "versions.yml:md5,975445af2def0ea44ea949ff5aee1fc0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T08:37:07.718649"
+    }
+}

modules/nf-core/geoquery/getgeo/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+    withName: 'GEOQUERY_GETGEO' {
+        ext.args = { "--metacols \"ID,ENTREZ_GENE_ID,Gene Symbol,Sequence Type\"" }
+        ext.prefix = { "${meta.id}." }
+    }
+}

tests/config/pytest_modules.yml

@@ -272,9 +272,6 @@ genotyphi/parse:
 genrich:
   - modules/nf-core/genrich/**
   - tests/modules/nf-core/genrich/**
-geoquery/getgeo:
-  - modules/nf-core/geoquery/getgeo/**
-  - tests/modules/nf-core/geoquery/getgeo/**
 gfaffix:
   - modules/nf-core/gfaffix/**
   - tests/modules/nf-core/gfaffix/**