Port parabricks/dbsnp to nf-test (#6977)

* port dbsnp * modify paths * modify paths * add process_gpu * update container * add snap * Update .github/workflows/test.yml * add stageInMode copy and snap * [automated] Fix linting with Prettier * remove old folder * remove test.yml * add to conda_skip * switch config and add tag gpu * update snap * Delete modules/nf-core/parabricks/dbsnp/tests/nextflow.config * Update modules/nf-core/parabricks/dbsnp/main.nf * Update modules/nf-core/parabricks/dbsnp/tests/main.nf.test --------- Co-authored-by: nf-core-bot <core@nf-co.re>
nf-core · Dec 11, 2024 · 356e5e6 · 356e5e6
1 parent a62c798
commit 356e5e6
Show file tree

Hide file tree

Showing 10 changed files with 126 additions and 62 deletions.
diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
@@ -182,6 +182,8 @@ 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/indexgvcf
   - profile: conda

diff --git a/modules/nf-core/parabricks/dbsnp/main.nf b/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}":

diff --git a/modules/nf-core/parabricks/dbsnp/tests/main.nf.test b/modules/nf-core/parabricks/dbsnp/tests/main.nf.test
@@ -0,0 +1,67 @@
+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") {
+
+        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() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap b/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"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -392,9 +392,6 @@ 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/**

diff --git a/tests/modules/nf-core/parabricks/dbsnp/main.nf b/tests/modules/nf-core/parabricks/dbsnp/main.nf
diff --git a/tests/modules/nf-core/parabricks/dbsnp/nextflow.config b/tests/modules/nf-core/parabricks/dbsnp/nextflow.config
diff --git a/tests/modules/nf-core/parabricks/dbsnp/test.yml b/tests/modules/nf-core/parabricks/dbsnp/test.yml
diff --git a/tests/modules/nf-core/parabricks/dbsnp/test_GPU_config.txt b/tests/modules/nf-core/parabricks/dbsnp/test_GPU_config.txt
diff --git a/tests/modules/nf-core/parabricks/dbsnp/test_GPU_yml.txt b/tests/modules/nf-core/parabricks/dbsnp/test_GPU_yml.txt