Optionally remove unmapped reads from downstream alignment outputs

[Joon-Klaps]

Description of feature

Add an opt-in parameter that drops unmapped reads from downstream alignment outputs to reduce storage and I/O overhead during polishing and consensus refinement.

See origial proposal in #280

Current behavior

Alignment outputs currently retain both mapped and unmapped reads. This preserves compatibility with existing runs, but it increases storage usage substantially for large datasets.

Proposal

• Add a new pipeline parameter, for example --remove_unmapped, defaulting to false.
• When enabled, filter downstream alignment outputs to mapped reads only, for example with samtools view -b -F 4, and index the filtered files.
• Keep the current behavior as the default for backwards compatibility.
• Update tests and documentation accordingly.