Merge branch 'master' into dbsnp

.github/conda_skip.yml

@@ -184,3 +184,5 @@ exclude:
     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/genotypegvcf/main.nf

@@ -2,7 +2,7 @@ process PARABRICKS_GENOTYPEGVCF {
     tag "$meta.id"
     label 'process_high'
 
-    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(input)
@@ -16,7 +16,6 @@ process PARABRICKS_GENOTYPEGVCF {
     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."
@@ -26,7 +25,6 @@ process PARABRICKS_GENOTYPEGVCF {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def output_file = "${prefix}.vcf"
     """
-
     pbrun \\
         genotypegvcf \\
         --ref $fasta \\

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

@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_GENOTYPEGVCF"
+    script "../main.nf"
+    process "PARABRICKS_GENOTYPEGVCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/genotypegvcf"
+    tag "gpu"
+
+    test("human - gvcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.variantsMD5,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("human - gvf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference'],
+                    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/parabricks/genotypegvcf/tests/main.nf.test.snap

@@ -0,0 +1,50 @@
+{
+    "human - gvcf": {
+        "content": [
+            "da770258f27bf3837c38769e9dfb1df3",
+            [
+                "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T12:09:42.000067144"
+    },
+    "human - gvf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T11:09:01.981995733"
+    }
+}

tests/config/pytest_modules.yml

@@ -398,9 +398,6 @@ oncocnv:
 parabricks/deepvariant:
   - modules/nf-core/parabricks/deepvariant/**
   - tests/modules/nf-core/parabricks/deepvariant/**
-parabricks/genotypegvcf:
-  - modules/nf-core/parabricks/genotypegvcf/**
-  - tests/modules/nf-core/parabricks/genotypegvcf/**
 parabricks/haplotypecaller:
   - modules/nf-core/parabricks/haplotypecaller/**
   - tests/modules/nf-core/parabricks/haplotypecaller/**