Port parabricks/dbsnp to nf-test

.github/conda_skip.yml

@@ -182,5 +182,7 @@ exclude:
     path: modules/nf-core/xeniumranger/resegment
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
+  - profile: conda
+    path: modules/nf-core/parabricks/dbsnp
   - profile: conda
     path: modules/nf-core/parabricks/genotypegvcf

modules/nf-core/parabricks/dbsnp/main.nf

@@ -1,8 +1,10 @@
 process PARABRICKS_DBSNP {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
+    stageInMode 'copy' // needed by the module to work properly - might be removed when this is fixed upstream
 
-    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+    container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"
 
     input:
     tuple val(meta), path(vcf_file), path(dbsnp_file), path(tabix_file)
@@ -15,22 +17,20 @@ process PARABRICKS_DBSNP {
     task.ext.when == null || task.ext.when
 
     script:
-
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def ann_vcf = "${prefix}.vcf"
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
-
     pbrun \\
         dbsnp \\
         --in-vcf $vcf_file \\
         --in-dbsnp-file $dbsnp_file \\
-        --out-vcf $ann_vcf \\
+        --out-vcf ${prefix}.vcf \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -42,9 +42,8 @@ process PARABRICKS_DBSNP {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def ann_vcf = "${prefix}.vcf"
     """
-    touch $ann_vcf
+    touch ${prefix}.vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/parabricks/dbsnp/tests/main.nf.test

@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_DBSNP"
+    script "../main.nf"
+    process "PARABRICKS_DBSNP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/dbsnp"
+    tag "gpu"
+
+    test("human - vcf") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.variantsMD5,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("human - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap

@@ -0,0 +1,50 @@
+{
+    "human - vcf": {
+        "content": [
+            "242dbff8325d7f958c95b34598146a0d",
+            [
+                "versions.yml:md5,08b9f4ea1507e634b70b8e0ab85ab536"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T14:17:11.379908895"
+    },
+    "human - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,08b9f4ea1507e634b70b8e0ab85ab536"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,08b9f4ea1507e634b70b8e0ab85ab536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T15:33:22.588142501"
+    }
+}

tests/config/pytest_modules.yml

@@ -395,9 +395,6 @@ ncbitools/vecscreen:
 oncocnv:
   - modules/nf-core/oncocnv/**
   - tests/modules/nf-core/oncocnv/**
-parabricks/dbsnp:
-  - modules/nf-core/parabricks/dbsnp/**
-  - tests/modules/nf-core/parabricks/dbsnp/**
 parabricks/deepvariant:
   - modules/nf-core/parabricks/deepvariant/**
   - tests/modules/nf-core/parabricks/deepvariant/**