add haplogrep3

modules/nf-core/haplogrep3/classify/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::haplogrep=3.2.2

modules/nf-core/haplogrep3/classify/main.nf

@@ -0,0 +1,47 @@
+process HAPLOGREP3_CLASSIFY {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/haplogrep3:3.2.2--hdfd78af_0':
+        'biocontainers/haplogrep3:3.2.2--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(inputfile)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    haplogrep3 \\
+        classify \\
+        $args \\
+        --in $inputfile \\
+        --out ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
+    END_VERSIONS
+    """
+
+}

modules/nf-core/haplogrep3/classify/meta.yml

@@ -0,0 +1,45 @@
+name: "haplogrep3_classify"
+description: classification into haplogroups
+keywords:
+  - haplogroups
+  - classify
+  - mtDNA
+tools:
+  - "haplogrep3":
+      description: "A tool for mtDNA haplogroup classification."
+      homepage: "https://github.com/genepi/haplogrep3"
+      documentation: "https://github.com/genepi/haplogrep3"
+      tool_dev_url: "https://github.com/genepi/haplogrep3"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - inputfile:
+        type: file
+        description: valid options are hsd, vcf, or fasta files
+        pattern: "*.{vcf,vcf.gz,fasta,hsd}"
+output:
+  - txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.txt":
+          type: file
+          description: text file with classification information
+          pattern: "*.{txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@lucpen"
+maintainers:
+  - "@lucpen"
+  - "@ramprasadn"

modules/nf-core/haplogrep3/classify/tests/main.nf.test

@@ -0,0 +1,59 @@
+
+nextflow_process {
+
+    name "Test Process HAPLOGREP3_CLASSIFY"
+    script "../main.nf"
+    process "HAPLOGREP3_CLASSIFY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "haplogrep3"
+    tag "haplogrep3/classify"
+
+    test("test-haplogrep3-classify") {
+
+        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/NA12878_chrM.vcf.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-haplogrep3-classify-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/NA12878_chrM.vcf.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-haplogrep3-classify-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-28T15:34:35.106097277"
+    },
+    "test-haplogrep3-classify": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,fb242df629aa6168371d1d742f0fb179"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,fb242df629aa6168371d1d742f0fb179"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-28T15:36:19.954363253"
+    }
+}

modules/nf-core/haplogrep3/classify/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: HAPLOGREP3_CLASSIFY {
+        ext.args = '--tree [email protected]'
+    }
+}