Add dedicated parameters for Trimmomatic adapter clipping

Currently, when using trimmomatic as trimming option in the MAG pipeline, there are no dedicated parameters (e.g., --trimmomatic_adapters) to specify adapter files or clipping settings. While Trimmomatic is supported as a module, users have to manually override ext.args via a custom config to enable ILLUMINACLIP.

I suggest adding a parameter that allows users to pass an adapter FASTA file and clipping constants directly via the command line or a pipeline specific config variable.

Ideally, the pipeline should handle:

Adapter File Path: A parameter like --trimmomatic_adapters that takes a path to a FASTA file.

Clipping Settings: Parameters for seed mismatches, palindrome clip threshold, and simple clip threshold (the 2:30:10 values).

I am currently using a custom config to inject the arguments:

process {
withName: 'TRIMMOMATIC' {
ext.args = 'ILLUMINACLIP:/path/to/adapter/NexteraPE-PE.fa:2:30:10'
}
}

Also this implementation would need to ensure that the specified adapter FASTA is correctly staged/mounted into the container environment, so that we may not have to give path to specific adapters.

Thanks

Start at the TRIMMOMATIC process and the pipeline-specific configuration or parameter entry points. Trace how ext.args is currently supplied and how input files are staged into the container. Done means adapter and clipping settings can be provided through the command line or pipeline config without manual ext.args overrides.