Add pcgr/getref module (#9295)

* Add pcgr/getref module

* fix meta and add stub snap

* comment out main test

Author: famosab

modules/nf-core/pcgr/getref/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::coreutils=9.5
+  - conda-forge::gzip=1.14
+  - conda-forge::tar=1.35
+  - conda-forge::curl=8.16.0

modules/nf-core/pcgr/getref/main.nf

@@ -0,0 +1,48 @@
+process PCGR_GETREF {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/517cc3a46129fc586191412f29246889124f4654640a53230aa203a2bcc1d7dc/data'
+        : 'community.wave.seqera.io/library/coreutils_curl_gzip_tar:17a6ea9a6766c02a'}"
+
+    input:
+    tuple val(meta), val(bundleversion), val(genome)
+
+    output:
+    tuple val(meta), path("${bundleversion}"), emit: pcgrref
+    path "versions.yml",                       emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def bundle = "pcgr_ref_data.${bundleversion}.${genome}.tgz"
+    """
+    curl -O https://insilico.hpc.uio.no/pcgr/${bundle}
+    gzip -dc ${bundle} | tar xvf -
+
+    mkdir ${bundleversion}
+    mv data/ ${bundleversion}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        curl: \$(curl --version | head -1 | cut -d ' ' -f 2)
+        tar: \$(tar --version | head -1 | cut -d ' ' -f 4)
+        gzip: \$(gzip --version | head -1 | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir ${bundleversion}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        curl: \$(curl --version | head -1 | cut -d ' ' -f 2)
+        tar: \$(tar --version | head -1 | cut -d ' ' -f 4)
+        gzip: \$(gzip --version | head -1 | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
+}

modules/nf-core/pcgr/getref/meta.yml

@@ -0,0 +1,59 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pcgr_getref"
+description: Get reference to run Personal Cancer Genome Reporter (PCGR)
+keywords:
+  - cancer
+  - reference
+  - pcgr
+  - mtb
+tools:
+  - pcgr:
+      description: "The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine"
+      homepage: "https://sigven.github.io/pcgr/index.html"
+      documentation: "https://sigven.github.io/pcgr/articles/running.html"
+      tool_dev_url: "https://github.com/sigven/pcgr/"
+      doi: "10.1093/bioinformatics/btx817"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bundleversion:
+        type: string
+        description: PCGR reference data bundle version
+        pattern: "*[0-9]*"
+        ontologies: []
+    - genome:
+        type: string
+        description: PCGR reference genome version
+        pattern: "grch37|grch38"
+        ontologies: []
+
+output:
+  pcgrref:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "${bundleversion}":
+          type: directory
+          description: PCGR reference data directory
+          pattern: "{bundleversion}/"
+          ontologies: []
+  versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"

modules/nf-core/pcgr/getref/tests/main.nf.test

@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process PCGR_GETREF"
+    script "../main.nf"
+    process "PCGR_GETREF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pcgr"
+    tag "pcgr/getref"
+
+    // test("human - 20250314 - grch38") {
+
+    //     when {
+    //         process {
+    //             """
+    //             input[0] = [
+    //                 [ id:'test' ],
+    //                 '20250314',
+    //                 'grch38'
+    //             ]
+    //             """
+    //         }
+    //     }
+
+    //     then {
+    //         assert process.success
+    //         assertAll(
+    //             { assert snapshot(
+    //                 process.out,
+    //                 path(process.out.versions[0]).yaml
+    //             ).match() }
+    //         )
+    //     }
+
+    // }
+
+    test("human - 20250314 - grch38 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    '20250314',
+                    'grch38'
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pcgr/getref/tests/main.nf.test.snap

@@ -0,0 +1,46 @@
+{
+    "human - 20250314 - grch38 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,25b668e4db59e455ba5a5b1fde55dc76"
+                ],
+                "pcgrref": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,25b668e4db59e455ba5a5b1fde55dc76"
+                ]
+            },
+            {
+                "PCGR_GETREF": {
+                    "curl": "8.16.0",
+                    "tar": 1.35,
+                    "gzip": 1.14
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T14:11:26.824317"
+    }
+}