Add dedicated parameters for Trimmomatic adapter clipping

[Pranjal-Bioinfo]

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