Added nf-test for krona/ktimporttaxonomy

nf-core · Jan 25, 2025 · 9b7a89b · 9b7a89b
1 parent 50a50b8
commit 9b7a89b
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Showing 9 changed files with 147 additions and 95 deletions.
diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf
@@ -40,7 +40,6 @@ process KRONA_KTIMPORTTAXONOMY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.8.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """

diff --git a/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test b/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test
@@ -1,6 +1,7 @@
 nextflow_process {
 
     name "Test Process KRONA_KTIMPORTTAXONOMY"
+    config "./nextflow.config"
     script "../main.nf"
     process "KRONA_KTIMPORTTAXONOMY"
 
@@ -9,53 +10,112 @@ nextflow_process {
     tag "krona"
     tag "krona/ktimporttaxonomy"
 
-    test ("sarscov2 - metagenome - kraken report") {
+
+
+    test("test_krona_ktimporttaxonomy_reads") {
 
         when {
+            params {
+                module_args = '-t 3'
+            }
             process {
                 """
-                input[0] = Channel.of([
-                   [id: 'test'],
-                   file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
-                ])
-                input[1] = Channel.of([
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
-                ])
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.reads.txt', checkIfExists: true)
+                    ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
                 """
             }
         }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.html[0][1]).text.contains('Severe acute respiratory syndrome-related coronavirus'),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
 
+
+    test("test_krona_ktimporttaxonomy_report") {
+
+        when {
+            params {
+                module_args = '-m 3 -t 5'
+            }
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
+                    ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
+                """
+            }
+        }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot ( process.out.versions ).match() },
-                { assert file(process.out.html.get(0).get(1)).exists() }
+                { assert snapshot(
+                    file(process.out.html[0][1]).text.contains('Severe acute respiratory syndrome-related coronavirus'),
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
 
-    test ("sarscov2 - metagenome - kraken report - stub") {
 
+    test("test_krona_ktimporttaxonomy_reads -- stub") {
         options '-stub'
         when {
+            params {
+                module_args = '-t 3'
+            }
             process {
                 """
-                input[0] = Channel.of([
-                   [id: 'test'],
-                   file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
-                ])
-                input[1] = Channel.of([
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
-                ])
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.reads.txt', checkIfExists: true)
+                    ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
                 """
             }
         }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 
+    test("test_krona_ktimporttaxonomy_report -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args = '-m 3 -t 5'
+            }
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
+                    ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
+                """
+            }
+        }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
-}
+}
diff --git a/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test.snap b/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test.snap
@@ -1,23 +1,25 @@
 {
-    "sarscov2 - metagenome - kraken report": {
+    "test_krona_ktimporttaxonomy_report": {
         "content": [
+            true,
             [
                 "versions.yml:md5,59fc89b6db8fad0aa9aa06f7437a18a7"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-08T10:34:23.760055"
+        "timestamp": "2025-01-25T19:59:51.434122"
     },
-    "sarscov2 - metagenome - kraken report - stub": {
+    "test_krona_ktimporttaxonomy_report -- stub": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "single_end": false
                         },
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -28,7 +30,8 @@
                 "html": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "single_end": false
                         },
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -39,9 +42,57 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-08T10:34:29.695251"
+        "timestamp": "2025-01-25T19:54:28.461618"
+    },
+    "test_krona_ktimporttaxonomy_reads": {
+        "content": [
+            true,
+            [
+                "versions.yml:md5,59fc89b6db8fad0aa9aa06f7437a18a7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-25T19:59:46.33943"
+    },
+    "test_krona_ktimporttaxonomy_reads -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,59fc89b6db8fad0aa9aa06f7437a18a7"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,59fc89b6db8fad0aa9aa06f7437a18a7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-25T19:54:23.95162"
     }
-}
+}
diff --git a/modules/nf-core/krona/ktimporttaxonomy/tests/nextflow.config b/modules/nf-core/krona/ktimporttaxonomy/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "KRONA_KTIMPORTTAXONOMY" {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/krona/ktimporttaxonomy/tests/tags.yml b/modules/nf-core/krona/ktimporttaxonomy/tests/tags.yml
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -254,9 +254,6 @@ krakentools/combinekreports:
 krona/kronadb:
   - modules/nf-core/krona/kronadb/**
   - tests/modules/nf-core/krona/kronadb/**
-krona/ktimporttaxonomy:
-  - modules/nf-core/krona/ktimporttaxonomy/**
-  - tests/modules/nf-core/krona/ktimporttaxonomy/**
 krona/ktimporttext:
   - modules/nf-core/krona/ktimporttext/**
   - tests/modules/nf-core/krona/ktimporttext/**

diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf
diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config b/tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config
diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/test.yml b/tests/modules/nf-core/krona/ktimporttaxonomy/test.yml
-Original file line number
+Diff line change
@@ Expand Up / @@ -40,7 +40,6 @@ process KRONA_KTIMPORTTAXONOMY { @@
         """
         stub:
-        def args = task.ext.args ?: ''
         def prefix = task.ext.prefix ?: "${meta.id}"
         def VERSION = '2.8.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
         """
@@ Expand Down @@