Added nf-test for gatk4/gatherpileupsummaries

modules/nf-core/gatk4/gatherpileupsummaries/main.nf

@@ -14,7 +14,7 @@ process GATK4_GATHERPILEUPSUMMARIES {
 
     output:
     tuple val(meta), path("*.pileups.table"), emit: table
-    path "versions.yml"                             , emit: versions
+    path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test

@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_GATHERPILEUPSUMMARIES"
+    script "../main.nf"
+    process "GATK4_GATHERPILEUPSUMMARIES"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/gatherpileupsummaries"
+
+    test("test-gatk4-gatherpileupsummaries") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ]
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap

@@ -0,0 +1,37 @@
+{
+    "test-gatk4-gatherpileupsummaries": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:18:40.835226"
+    }
+}

tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config → modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config

@@ -1,7 +1,4 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'GATK4_GATHERPILEUPSUMMARIES' {
         ext.prefix       = { "${meta.id}.out" }
     }

tests/config/pytest_modules.yml

@@ -476,9 +476,6 @@ gatk4/filtervarianttranches:
 gatk4/gatherbqsrreports:
   - modules/nf-core/gatk4/gatherbqsrreports/**
   - tests/modules/nf-core/gatk4/gatherbqsrreports/**
-gatk4/gatherpileupsummaries:
-  - modules/nf-core/gatk4/gatherpileupsummaries/**
-  - tests/modules/nf-core/gatk4/gatherpileupsummaries/**
 gatk4/genotypegvcfs:
   - modules/nf-core/gatk4/genotypegvcfs/**
   - tests/modules/nf-core/gatk4/genotypegvcfs/**