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

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

@@ -2,7 +2,7 @@ process PARABRICKS_DEEPVARIANT {
     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), path(input_index), path(interval_file)
@@ -16,25 +16,23 @@ process PARABRICKS_DEEPVARIANT {
     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 ?: "${meta.id}"
-    def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf"
+    def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf" : "${prefix}.vcf"
     def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
-
     pbrun \\
         deepvariant \\
         --ref $fasta \\
         --in-bam $input \\
         --out-variants $output_file \\
         $interval_file_command \\
-        --num-gpus $task.accelerator.request \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -44,9 +42,8 @@ process PARABRICKS_DEEPVARIANT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf"
+    def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf" : "${prefix}.vcf"
     """
     touch $output_file
 

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

@@ -0,0 +1,178 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_DEEPVARIANT"
+    script "../main.nf"
+    process "PARABRICKS_DEEPVARIANT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/deepvariant"
+    tag "gpu"
+
+    test("human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    [], // bam.bai not needed unless using intervals
+                    []
+                ]
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/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 - bam - intervals") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'ref'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/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 - bam - intervals - gvcf") {
+
+        config './nextflow.config'
+
+        when {
+            params {
+                 module_args = '--gvcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'ref'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    // file(process.out.vcf[0][1]).name // fails with groovy.lang.MissingMethodException: No signature of method: static com.askimed.nf.test.lang.extensions.GlobalMethods.file() is applicable for argument types: (ArrayList) values:
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    [], // bam.bai not needed unless using intervals
+                    []
+                ]
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - bam - intervals - gvcf - stub") {
+
+        config './nextflow.config'
+        options "-stub"
+
+        when {
+            params {
+                 module_args = '--gvcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,106 @@
+{
+    "human - bam - intervals - gvcf": {
+        "content": [
+            [
+                "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T15:26:48.481295634"
+    },
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T15:05:28.449273519"
+    },
+    "human - bam - intervals": {
+        "content": [
+            "27097afc7aae62918a3e26790cc189c3",
+            [
+                "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T15:06:52.854870182"
+    },
+    "human - bam": {
+        "content": [
+            "8b526a232f93a5036176336415abf7d1",
+            [
+                "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T15:06:37.651354312"
+    },
+    "human - bam - intervals - gvcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T15:12:11.438654866"
+    }
+}

modules/nf-core/parabricks/deepvariant/tests/nextflow.config

@@ -0,0 +1,8 @@
+process {
+
+    withName: 'PARABRICKS_DEEPVARIANT' {
+        ext.args = params.module_args
+        stageInMode = 'copy'
+    }
+
+}

tests/config/pytest_modules.yml

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