Added nf-test for yahs

modules/nf-core/yahs/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/c-zhou/yahs"
       tool_dev_url: "https://github.com/c-zhou/yahs"
       doi: "10.1093/bioinformatics/btac808"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta:

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

@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+    name "Test Process YAHS"
+    script "../main.nf"
+    process "YAHS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "yahs"
+
+    test("test-yahs") {
+
+        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.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,67 @@
+{
+    "test-yahs": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bin:md5,c60503a616a0f7726176febdad3ae186"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,007c44dd06fe8686b6f8068314601462"
+                ],
+                "binary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bin:md5,c60503a616a0f7726176febdad3ae186"
+                    ]
+                ],
+                "scaffolds_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168"
+                    ]
+                ],
+                "scaffolds_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,007c44dd06fe8686b6f8068314601462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T08:47:14.869961"
+    }
+}

tests/modules/nf-core/yahs/nextflow.config → modules/nf-core/yahs/tests/nextflow.config

@@ -1,10 +1,6 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'test_yahs:YAHS' {
         ext.prefix = { "${meta.id}" }
         ext.args = '--no-contig-ec'
     }
-
 }

tests/config/pytest_modules.yml

@@ -1665,6 +1665,3 @@ wgsim:
 whamg:
   - modules/nf-core/whamg/**
   - tests/modules/nf-core/whamg/**
-yahs:
-  - modules/nf-core/yahs/**
-  - tests/modules/nf-core/yahs/**