Optionally use host-filtered reads in downstream mapping steps

[Joon-Klaps]

Description of feature

Add an opt-in parameter to use host-filtered or host-depleted FASTQ files for downstream mapping and polishing steps when those files are available.

See original proposal in #280

Current behavior

Downstream steps such as sspace_basic, bwamem2, and bowtie2 currently use the original clean FASTQ files. This preserves current behavior, but it can increase runtime and storage usage substantially on large datasets.

Proposal

• Add a new pipeline parameter, defaulting to false.
• When enabled, prefer host-filtered reads for downstream mapping and polishing steps after host subtraction has completed successfully.
• Keep the current clean-read behavior as the default for backwards compatibility.
• Update tests and documentation accordingly.