Alejandro Bernabeu issues

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                                            Alejandro Bernabeu

Add results per sample to `summary_report_pid.py`

### PR Description Updated `summary_to_tab_group` in `summary_report_pid.py` to generate a second report where plasmid identification results are organized `per sample`. **Reasoning:** The previous implementation did not provide plasmid identification results...

Replace local `snpeff_ann` module with `nf-core/snpeff/snpeff`

## PR Description This PR replaces the legacy local module snpeff_ann with the standardized nf-core/snpeff/snpeff module from the nf-core/modules repository. **Changes made:** - Replaced the local process snpeff_ann.nf with the...