Add new refinegems nf-core module with config-generation interface

modules/nf-core/refinegems/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::python=3.10.19
+  - conda-forge::pip=25.2
+  - pip:
+      - refineGEMs==0.1.23

modules/nf-core/refinegems/main.nf

@@ -0,0 +1,45 @@
+process REFINEGEMS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.10.16' :
+        'docker.io/library/python:3.10-slim' }"
+
+    input:
+    tuple val(meta), val(config_type)
+
+    output:
+    tuple val(meta), path("*.yaml"), emit: yaml
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    refinegems setup config \\
+        --type ${config_type} \\
+        --filename ${prefix}.yaml \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        refinegems: \$(refinegems --version | sed -E 's/.*([0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?).*/\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.yaml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        refinegems: 0.1.23
+    END_VERSIONS
+    """
+}

modules/nf-core/refinegems/meta.yml

@@ -0,0 +1,48 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "refinegems"
+description: Download a default refineGEMs configuration YAML file.
+keywords:
+  - config
+  - yaml
+  - metabolic model
+  - genome-scale metabolic model
+tools:
+  - refinegems:
+      description: A toolbox for fast curation and analysis of genome-scale metabolic models.
+      homepage: https://github.com/draeger-lab/refinegems
+      documentation: https://refinegems.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/draeger-lab/refinegems
+      licence: ["MIT"]
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - config_type:
+        type: string
+        description: Type of config file to download. One of `media` or `refinegems`.
+output:
+  yaml:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.yaml":
+          type: file
+          description: A refineGEMs configuration YAML file.
+          pattern: "*.yaml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@brovolia"
+maintainers:
+  - "@brovolia"

modules/nf-core/refinegems/tests/main.nf.test

@@ -0,0 +1,30 @@
+nextflow_process {
+
+    name "Test Process REFINEGEMS"
+    script "../main.nf"
+    process "REFINEGEMS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "refinegems"
+
+    test("test-refinegems-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], 'refinegems' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/refinegems/tests/main.nf.test.snap

@@ -0,0 +1,37 @@
+{
+    "test-refinegems-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,998d15a0141fca0a296d2b5e50e95a40"
+                ],
+                "yaml": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,998d15a0141fca0a296d2b5e50e95a40"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2026-06-09T10:30:00.000000"
+    }
+}