Added nf-test for paragraph/vcf2paragraph

modules/nf-core/paragraph/vcf2paragraph/environment.yml

@@ -1,7 +1,10 @@
 name: paragraph_vcf2paragraph
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
+  - bioconda::htslib=1.10.2
   - bioconda::paragraph=2.3

modules/nf-core/paragraph/vcf2paragraph/main.nf

@@ -48,7 +48,7 @@ process PARAGRAPH_VCF2PARAGRAPH {
     def VERSION = '2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
-    touch ${prefix}.json.gz
+    echo | gzip > ${prefix}.json.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/paragraph/vcf2paragraph/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/Illumina/paragraph"
       tool_dev_url: "https://github.com/Illumina/paragraph"
       doi: "10.1101/635011"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map

modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test

@@ -0,0 +1,64 @@
+
+nextflow_process {
+
+    name "Test Process PARAGRAPH_VCF2PARAGRAPH"
+    script "../main.nf"
+    process "PARAGRAPH_VCF2PARAGRAPH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "paragraph"
+    tag "paragraph/vcf2paragraph"
+
+    test("test-paragraph-vcf2paragraph") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true)
+				]
+				input[1] = [ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.graph,
+                    process.out.versions,
+                    file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-paragraph-vcf2paragraph-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true)
+				]
+				input[1] = [ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test.snap

@@ -0,0 +1,63 @@
+{
+    "test-paragraph-vcf2paragraph": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.json.gz:md5,68dce3f3713b691f9ab45744500871bf"
+                ]
+            ],
+            [
+                "versions.yml:md5,a7024dd35463d16da31df17264fdad6d"
+            ],
+            [
+                "\"PARAGRAPH_VCF2PARAGRAPH\":",
+                "paragraph: 2.3",
+                "bgzip: 1.10.2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-30T10:55:01.125722"
+    },
+    "test-paragraph-vcf2paragraph-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a7024dd35463d16da31df17264fdad6d"
+                ],
+                "graph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a7024dd35463d16da31df17264fdad6d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-29T16:42:34.344697"
+    }
+}

tests/config/pytest_modules.yml

@@ -716,9 +716,6 @@ paragraph/idxdepth:
 paragraph/multigrmpy:
   - modules/nf-core/paragraph/multigrmpy/**
   - tests/modules/nf-core/paragraph/multigrmpy/**
-paragraph/vcf2paragraph:
-  - modules/nf-core/paragraph/vcf2paragraph/**
-  - tests/modules/nf-core/paragraph/vcf2paragraph/**
 pbbam/pbmerge:
   - modules/nf-core/pbbam/pbmerge/**
   - tests/modules/nf-core/pbbam/pbmerge/**