ADD CATPACK_DOWNLOAD

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

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::cat=6.0.1"

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

@@ -0,0 +1,47 @@
+process CATPACK_DOWNLOAD {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/cat:6.0.1--hdfd78af_0'
+        : 'biocontainers/cat:6.0.1--hdfd78af_0'}"
+
+    input:
+    tuple val(meta), val(db)
+
+    output:
+    tuple val(meta), path("${db}/"), emit: rawdb
+    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}"
+    """
+    CAT_pack \\
+        download \\
+        ${args} \\
+        --db ${db}
+        -o ${prefix}/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        catpack: \$(CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        catpack: \$(CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,51 @@
+---
+name: "catpack_download"
+description: Downloads the required files for either Nr or GTDB for building into a CAT database
+keywords:
+  - taxonomic classification
+  - classification
+  - database
+  - download
+tools:
+  - "catpack":
+      description: "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)"
+      homepage: "https://github.com/MGXlab/CAT_pack"
+      documentation: "https://github.com/MGXlab/CAT_pack"
+      tool_dev_url: "https://github.com/MGXlab/CAT_pack"
+      doi: "10.1186/s13059-019-1817-x"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - db:
+        type: string
+        description: Which database to download
+        pattern: "nr|gtdb"
+
+output:
+  - rawdb:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${db}/":
+          type: directory
+          description: Directory containing all the required NCBI Nr or GTDB database files required for building into a CAT database
+          pattern: "${db}/"
+          ontologies:
+            - edam: "http://edamontology.org/data_1049"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@jfy133"
+maintainers:
+  - "@jfy133"

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

@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test Process CATPACK_DOWNLOAD"
+    script "../main.nf"
+    process "CATPACK_DOWNLOAD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "catpack"
+    tag "catpack/download"
+
+    // Only stub because module downloads extremely large
+    test("nr - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'nr', single_end:false ], // meta map
+                    'nr',
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,41 @@
+{
+    "nr - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "nr",
+                            "single_end": false
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e1493fe75b3b8cc2bc0cbd1d5ddfad44"
+                ],
+                "rawdb": [
+                    [
+                        {
+                            "id": "nr",
+                            "single_end": false
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1493fe75b3b8cc2bc0cbd1d5ddfad44"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T16:19:22.533589236"
+    }
+}

modules/nf-core/coptr/estimate/meta.yml

@@ -28,7 +28,7 @@ input:
         description: Python pickle file containing coverage maps
         pattern: "*.pkl"
         ontologies:
-            - edam: "http://edamontology.org/format_4002"
+          - edam: "http://edamontology.org/format_4002"
 
 output:
   - ptr:
@@ -42,7 +42,7 @@ output:
           description: CSV table with rows as reference genomes, columns samples and entries as log2 PTR
           pattern: "*.csv"
           ontologies:
-              - edam: "http://edamontology.org/format_3752"
+            - edam: "http://edamontology.org/data_3752"
 
   - versions:
       - "versions.yml":