Added nf-test for verifybamid/verifybamid

modules/nf-core/verifybamid/verifybamid/environment.yml

@@ -1,4 +1,4 @@
-name: VERIFYBAMID_VERIFYBAMID
+name: verifybamid_verifybamid
 channels:
   - conda-forge
   - bioconda

modules/nf-core/verifybamid/verifybamid/meta.yml

@@ -1,4 +1,4 @@
-name: "VERIFYBAMID_VERIFYBAMID"
+name: "verifybamid_verifybamid"
 description: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
 keywords:
   - qc
@@ -11,7 +11,7 @@ tools:
       documentation: "http://genome.sph.umich.edu/wiki/VerifyBamID"
       tool_dev_url: "https://github.com/statgen/verifyBamID"
       doi: "10.1016/j.ajhg.2012.09.004"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

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

@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+    name "Test Process VERIFYBAMID_VERIFYBAMID"
+    script "../main.nf"
+    process "VERIFYBAMID_VERIFYBAMID"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "verifybamid"
+    tag "verifybamid/verifybamid"
+
+    test("test-verifybamid-verifybamid") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.depthrg,
+                    process.out.depthsm,
+                    process.out.selfrg,
+                    process.out.selfsm,
+                    process.out.versions,
+                    ).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,51 @@
+{
+    "test-verifybamid-verifybamid": {
+        "content": [
+            "test.log",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.depthRG:md5,2374504c4138c04f3b29210dcb3da96f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.depthSM:md5,4f5367f2be8567b95b57278b2e7372c3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.selfRG:md5,3772283d3eaa88683f562a2157b92d55"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.selfSM:md5,5d2808d70f76e2f753b670fc9b2a6d55"
+                ]
+            ],
+            [
+                "versions.yml:md5,36b44d66ecfdbef7191f47a33f688b7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:54:07.273193"
+    }
+}

modules/nf-core/verifybamid/verifybamid/tests/nextflow.config

@@ -0,0 +1,3 @@
+process {
+        ext.args = '--ignoreRG'
+}

tests/config/pytest_modules.yml

@@ -1641,9 +1641,6 @@ vcflib/vcffilter:
 vcflib/vcfuniq:
   - modules/nf-core/vcflib/vcfuniq/**
   - tests/modules/nf-core/vcflib/vcfuniq/**
-verifybamid/verifybamid:
-  - modules/nf-core/verifybamid/verifybamid/**
-  - tests/modules/nf-core/verifybamid/verifybamid/**
 verifybamid/verifybamid2:
   - modules/nf-core/verifybamid/verifybamid2/**
   - tests/modules/nf-core/verifybamid/verifybamid2/**