Add MacSyFinder modules for model management and protein system detection

[Copilot]

Adds support for MacSyFinder, a tool for detecting macromolecular systems in protein datasets using HMM-based similarity search.

Implementation

Two submodules following the tool's workflow:

• macsyfinder/download: Fetches models via macsydata

  • Input: model name (e.g., 'TXSScan', 'CasFinder')
  • Output: models directory

• macsyfinder/search: Executes system detection

  • Input: protein FASTA, models directory, optional model filter
  • Output: summary TSV, best solutions, complete results directory
  • Supports multiple database types: gembase (default), ordered_replicon, unordered

Usage

include { MACSYFINDER_DOWNLOAD } from './modules/nf-core/macsyfinder/download/main'
include { MACSYFINDER_SEARCH } from './modules/nf-core/macsyfinder/search/main'

MACSYFINDER_DOWNLOAD('TXSScan')

input_ch = Channel.of([
    [id: 'sample1', db_type: 'gembase'],
    file('proteins.faa')
])

MACSYFINDER_SEARCH(
    input_ch,
    MACSYFINDER_DOWNLOAD.out.models,
    'TXSScan'
)

Technical Details

• Container: macsyfinder:2.1.6 from biocontainers
• Both modules include complete meta.yml documentation and nf-test definitions
• Search module captures HMMER version alongside MacSyFinder

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• api.anaconda.org
  • Triggering command: /usr/bin/curl curl -s REDACTED (dns block)
• get.nextflow.io
  • Triggering command: /usr/bin/curl curl -s REDACTED (dns block)
• https://api.github.com/repos/gem-pasteur/macsyfinder
  • Triggering command: /usr/bin/curl curl -s REDACTED (http block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>new module: macsyfinder</issue_title>
<issue_description>### Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

MacSyFinder is a tool for detection of macromolecular systems in protein datasets using systems modelling and similarity search.

GitHub repo: https://github.com/gem-pasteur/macsyfinder

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module</issue_description>

<agent_instructions>Macsyfinder is compatible with models, they are here. We need to build models first and then run Macsyfinder, so it will be several sunmodules</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes new module: macsyfinder #10073

---

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[SPPearce]

@copilot , please take a look at this: https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules and ensure that you use the topic channel to emit the versions, rather than creating the versions.yml

[brovolia]

Hi @SPPearce, thanks for pointing this! I've already modified it in my local environment. Could you kindly review this PR? Btw do you know how to fix the error from linter, which tells that md5sun for empty file is found? MSF produces this empty .err files intentionally and I can't change it

[mashehu]

to fix the linting error make sure that the file is actually emtpy (with path(.out.err).text == "" please add the full channel name there).

[mashehu]

this PR is also missing snapshot files

[brovolia]

Sure, after linting my changes, I will push the snapshots here

[LouisLeNezet]

To fix the meta.yml you can use nf-core modules lint --fix module_name

Here is a few comment to improve the process.

[LouisLeNezet]

You can simplify by

Suggested change

	tuple val("${task.process}"), val('macsyfinder'), eval('macsyfinder --version 2>&1 | head -1 | sed "s/^.*MacSyFinder //; s/ .*$//"'), topic: versions, emit: versions_macsyfinder
	tuple val("${task.process}"), val('macsyfinder'), eval('macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//"'), topic: versions, emit: versions_macsyfinder

[LouisLeNezet]

This is not something that we usually do.
Is is a necessary input or is it optional.
If so either pass it through external arguments or via a dedicated value channel.

[LouisLeNezet]

Please improve as recommended above 😉

[brovolia]

I tried with automatic --fix, but it adds me the curly brackets and makes smth weird with my meta.yml. I am stucked here

[LouisLeNezet]

I tried with automatic --fix, but it adds me the curly brackets and makes smth weird with my meta.yml. I am stucked here

The {} does sometimes happen. You just need to copy paste back what was inside.