nf-core modules lint fails on patched modules with modified inputs/outputs

[svarona]

Description of the bug

There is a problem with nf-core modules lint when working with patched modules that require different inputs or outputs compared to the original module.

Steps to reproduce:

1. Change a module (e.g. artic/minion, cutadapt, multiqc) to use different inputs/outputs.
2. Run nf-core modules lint --fix. This adds those new inputs/outputs to the meta.yml without description (fix the fields in the yml file)
3. Run nf-core modules patch so that the meta.yml changes are reflected in the .diff file.
4. Run nf-core modules lint

If I remove the additional inputs/outputs, the linting passes, but this defeats the purpose of the patch.
This seems to be a recurring issue across pipelines whenever there is a patch with modified inputs/outputs.

Command used and terminal output

$nf-core modules lint
╭─ [✗] 3 Module Tests Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                ╷                                       ╷                                                                                                                                                                                                                                            │
│ Module name                    │ File path                             │ Test message                                                                                                                                                                                                                               │
│╶───────────────────────────────┼───────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ artic/minion                   │ modules/nf-core/artic/minion/meta.yml │ Module meta.yml does not match main.nf. Inputs should contain: [['meta', 'fastq'], 'fast5_dir', 'sequencing_summary', 'primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta',                                             │
│                                │                                       │ 'primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed', 'medaka_model_file', 'medaka_model_string', 'scheme', 'scheme_version'] Run nf-core modules lint --fix to update the meta.yml file.                                    │
│ cutadapt                       │ modules/nf-core/cutadapt/meta.yml     │ Module meta.yml does not match main.nf. Inputs should contain: [['meta', 'reads'], 'adapters'] Run nf-core modules lint --fix to update the meta.yml file.                                                                                 │
│ multiqc                        │ modules/nf-core/multiqc/meta.yml      │ Module meta.yml does not match main.nf. Outputs should contain: {'report': ['multiqc_report.html'], 'data': ['_data'], 'plots': ['_plots'], 'csv_reports': ['.csv'], 'versions': ['versions.yml']} Run nf-core modules lint --fix to       │
│                                │                                       │ update the meta.yml file.                                                                                                                                                                                                                  │
│                                ╵                                       ╵                                                                                                                                                                                                                                            │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

System information

N E X T F L O W versions 25.04.6 and 25.04.7
Hardware : HPC and Desktop
Executor: Slurm and local
OS: CentOS Stream release 8 and Ubuntu 22.04.5 LTS
Version of nf-core/tools: 3.3.2
Python version: 3.12.11