Add MacSyFinder modules for model management and protein system detection

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

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::macsyfinder=2.1.6

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

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+process MACSYFINDER_DOWNLOAD {
+    tag "${model_name}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/macsyfinder:2.1.6--pyhdfd78af_0' :
+        'biocontainers/macsyfinder:2.1.6--pyhdfd78af_0' }"
+
+    input:
+    val model_name
+
+    output:
+    path "models"       , emit: models
+    tuple val("${task.process}"), val('macsyfinder'), eval('macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//"'), topic: versions, emit: versions_macsyfinder
+    tuple val("${task.process}"), val('msf_data'), eval('msf_data --version 2>&1 | awk "NR==4{print \$2}"'), topic: versions, emit: versions_macsydata
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    # msf_data installs models into the current directory by default
+    # We'll create a models directory to store them
+    mkdir -p models
+
+    msf_data install \\
+        --target models \\
+        ${args} \\
+        ${model_name}
+    """
+
+    stub:
+    """
+    mkdir -p models/${model_name}
+    touch models/${model_name}/definitions.txt
+    """
+}

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

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+name: "macsyfinder_download"
+description: Download MacSyFinder models using msf_data
+keywords:
+  - genomics
+  - protein
+  - macromolecular systems
+  - models
+  - database
+tools:
+  - "macsyfinder":
+      description: "Detection of macromolecular systems in protein datasets using systems\
+        \ modelling and similarity search"
+      homepage: "https://github.com/gem-pasteur/macsyfinder"
+      documentation: "https://macsyfinder.readthedocs.io"
+      tool_dev_url: "https://github.com/gem-pasteur/macsyfinder"
+      doi: "10.24072/pcjournal.250"
+      licence:
+        - "GPL v3"
+      identifier: biotools:macsyfinder
+input:
+  - model_name:
+      type: string
+      description: Name of the MacSyFinder model to download (e.g., 'TXSScan', 'CasFinder')
+output:
+  models:
+    - models:
+        type: directory
+        description: Directory containing downloaded MacSyFinder model definitions
+        pattern: "models"
+  versions_macsyfinder:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_macsydata:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - msf_data:
+          type: string
+          description: The name of the tool
+      - msf_data --version 2>&1 | awk "NR==4{print \$2}":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - msf_data:
+          type: string
+          description: The name of the tool
+      - msf_data --version 2>&1 | awk "NR==4{print \$2}":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@brovolia"
+maintainers:
+  - "@brovolia"

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

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+nextflow_process {
+
+    name "Test Process MACSYFINDER_DOWNLOAD"
+    script "../main.nf"
+    process "MACSYFINDER_DOWNLOAD"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "macsyfinder"
+    tag "macsyfinder/download"
+
+    test("macsyfinder_download - TXSScan") {
+
+        when {
+            process {
+                """
+                input[0] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match("txsscan_output") },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("txsscan_versions") }
+            )
+        }
+    }
+
+    test("macsyfinder_download - TXSScan - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match("txsscan_stub_output") },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("txsscan_stub_versions") }
+            )
+        }
+    }
+}