Added nf-test for vcflib/vcffilter

modules/nf-core/vcflib/vcffilter/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/vcflib/vcflib"
       tool_dev_url: "https://github.com/vcflib/vcflib"
       doi: "10.1371/journal.pcbi.1009123"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/nf-core/vcflib/vcffilter/tests/main.nf.test

@@ -0,0 +1,41 @@
+
+nextflow_process {
+
+    name "Test Process VCFLIB_VCFFILTER"
+    script "../main.nf"
+    process "VCFLIB_VCFFILTER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vcflib"
+    tag "vcflib/vcffilter"
+
+    test("test-vcflib-vcffilter") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.vcf[0][1]).vcf.variantsMD5,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/vcflib/vcffilter/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "test-vcflib-vcffilter": {
+        "content": [
+            "9c77022b6e4117314e02ff889f56c292",
+            [
+                "versions.yml:md5,1867ed263ff722a16dd0f77cea80ab65"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-27T11:48:33.121349"
+    }
+}

tests/modules/nf-core/vcflib/vcffilter/nextflow.config → modules/nf-core/vcflib/vcffilter/tests/nextflow.config

@@ -1,8 +1,4 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-
     withName: VCFLIB_VCFFILTER {
         ext.args = '-f "DP > 4"'
         ext.prefix = 'filtered'

tests/config/pytest_modules.yml

@@ -1368,9 +1368,6 @@ vcf2maf:
 vcflib/vcfbreakmulti:
   - modules/nf-core/vcflib/vcfbreakmulti/**
   - tests/modules/nf-core/vcflib/vcfbreakmulti/**
-vcflib/vcffilter:
-  - modules/nf-core/vcflib/vcffilter/**
-  - tests/modules/nf-core/vcflib/vcffilter/**
 verifybamid/verifybamid2:
   - modules/nf-core/verifybamid/verifybamid2/**
   - tests/modules/nf-core/verifybamid/verifybamid2/**