port parabricks/indexgvcf 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/indexgvcf
   - profile: conda
     path: modules/nf-core/parabricks/genotypegvcf

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

@@ -1,16 +1,17 @@
 process PARABRICKS_INDEXGVCF {
     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(gvcf, stageAs:'')
+    tuple val(meta), path(gvcf)
 
     output:
-    // This tool outputs g.vcf.idx if input is uncompressed, g.vcf.gz.tbi if input is compressed
-    tuple val(meta), path("*.g.vcf*") , emit: gvcf_index
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*.{idx,tbi}") , emit: gvcf_index
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,12 +22,12 @@ process PARABRICKS_INDEXGVCF {
         error "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 num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     pbrun \\
         indexgvcf \\
         --input $gvcf \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,19 +40,10 @@ process PARABRICKS_INDEXGVCF {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "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 output_cmd = gvcf.any{ it.name.endsWith(".gz") } ? "touch ${prefix}.g.vcf.gz.tbi" : "touch ${prefix}.g.vcf.idx"
     """
-    # Different outputs generated depending if file is gzipped
-    case $gvcf in
-    *.gz )
-        touch ${prefix}.g.vcf.gz.tbi
-        ;;
-    * )
-        touch ${prefix}.g.vcf.idx
-        ;;
-    esac
+    $output_cmd
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/parabricks/indexgvcf/meta.yml

@@ -30,9 +30,11 @@ output:
           type: map
           description: |
             Groovy Map containing output information
-      - "*.g.vcf*":
-          type: file
-          description: Indexed gvcf file
+          pattern: "*.g.vcf"
+      - "*.{idx,tbi}":
+          type: map
+          description: |
+            Groovy Map containing output information
           pattern: "*.g.vcf"
   - versions:
       - versions.yml:

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

@@ -0,0 +1,109 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_INDEXGVCF"
+    script "../main.nf"
+    process "PARABRICKS_INDEXGVCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/indexgvcf"
+    tag "gpu"
+
+    test("human - gvcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.gvcf_index[0][1]).name,
+                    process.out.versions
+                    ).match() 
+                }
+            )
+        }
+
+    }
+
+    test("human - gvcf.gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - gvcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - gvcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,114 @@
+{
+    "human - gvcf.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:16:48.994612337"
+    },
+    "human - gvcf": {
+        "content": [
+            "test.genome.g.vcf.idx",
+            [
+                "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:21:20.010561875"
+    },
+    "human - gvcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:21:32.292223281"
+    },
+    "human - gvcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:14:58.744532337"
+    }
+}

tests/config/pytest_modules.yml

@@ -401,9 +401,6 @@ parabricks/deepvariant:
 parabricks/haplotypecaller:
   - modules/nf-core/parabricks/haplotypecaller/**
   - tests/modules/nf-core/parabricks/haplotypecaller/**
-parabricks/indexgvcf:
-  - modules/nf-core/parabricks/indexgvcf/**
-  - tests/modules/nf-core/parabricks/indexgvcf/**
 parabricks/mutectcaller:
   - modules/nf-core/parabricks/mutectcaller/**
   - tests/modules/nf-core/parabricks/mutectcaller/**