New module: busco/download

modules/nf-core/busco/download/environment.yml

@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::busco=5.8.2

modules/nf-core/busco/download/main.nf

@@ -0,0 +1,48 @@
+process BUSCO_DOWNLOAD {
+    tag "$lineage"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0':
+        'biocontainers/busco:5.8.2--pyhdfd78af_0' }"
+
+    input:
+    val lineage
+
+    output:
+    path "busco_downloads", emit: download_dir
+    path "versions.yml"   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${lineage}"
+    """
+    busco \\
+        --download $lineage \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    echo "busco \\
+        --download $lineage \\
+        $args"
+
+    mkdir busco_downloads
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
+    """
+}

modules/nf-core/busco/download/meta.yml

@@ -0,0 +1,38 @@
+name: busco_download
+description: Download database for BUSCO
+keywords:
+  - quality control
+  - genome
+  - transcriptome
+  - proteome
+tools:
+  - busco:
+      description: BUSCO provides measures for quantitative assessment of genome assembly,
+        gene set, and transcriptome completeness based on evolutionarily informed expectations
+        of gene content from near-universal single-copy orthologs selected from OrthoDB.
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      tool_dev_url: https://gitlab.com/ezlab/busco
+      doi: "10.1007/978-1-4939-9173-0_14"
+      licence: ["MIT"]
+      identifier: biotools:busco
+input:
+  - - lineage:
+        type: string
+        description: The BUSCO lineage to use, or "auto", "auto_prok" or "auto_euk"
+          to automatically select lineage
+output:
+  - download_dir:
+      - busco_downloads:
+          type: file
+          description: Directory with busco database
+          pattern: "busco_downloads"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@zachary-foster"
+maintainers:
+  - "@zachary-foster"

modules/nf-core/busco/download/tests/main.nf.test

@@ -0,0 +1,53 @@
+nextflow_process {
+
+    name "Test Process BUSCO_DOWNLOAD"
+    script "../main.nf"
+    process "BUSCO_DOWNLOAD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "busco"
+    tag "busco/download"
+
+    test("BUSCO database download") {
+
+        when {
+            process {
+                """
+                input[0] = [ 'eukaryota_odb10' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.download_dir.get(0)).exists() },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+    test("BUSCO database download - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ 'stub' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/busco/download/tests/main.nf.test.snap

@@ -0,0 +1,41 @@
+{
+    "BUSCO database download": {
+        "content": [
+            [
+                "versions.yml:md5,48283b252a072b5cc4054d311e315c10"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-12T13:48:41.389560409"
+    },
+    "BUSCO database download - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,48283b252a072b5cc4054d311e315c10"
+                ],
+                "download_dir": [
+                    [
+
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,48283b252a072b5cc4054d311e315c10"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-12T17:24:32.861082849"
+    }
+}

modules/nf-core/busco/download/tests/tags.yml

@@ -0,0 +1,2 @@
+busco/download:
+  - "modules/nf-core/busco/download/**"