feat: integrate workflow cache for bowtie indexes#182
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- derive cache keys from workflow-owned Bowtie2 index parameters - build and materialize reference and subtraction indexes through WorkflowCache - use the local VIR-2315 Virtool worktree for cache client support
- Restore cached indexes directly into the workflow target directory. - Use keyed local staging paths for cache misses to avoid deleting staged artifacts.
- Build and restore reference indexes into a dedicated workflow output folder. - Build and restore subtraction indexes into per-subtraction output folders consumed by elimination.
- fetch the bowtie2-build version inside cache param construction - keep cache key tests aligned with the live tool-version source
- assemble the reference FASTA from reference JSON before bowtie2-build - include the default-isolate source contract in reference index cache params
- inline cache hit and miss handling for reference and subtraction indexes - keep the shared Bowtie helper focused on invoking bowtie2-build - read reference FASTA input from index.json_path directly
- build subtraction indexes before elimination through a dedicated step - pass subtraction index paths into downstream elimination instead of rebuilding them
- keep workflow step definitions focused on orchestration - expose cache parameter helpers from workflow_pathoscope.utils for tests
- build reference index inputs from a temporary FASTA path - derive subtraction index paths from the shared indexes directory
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derive cache keys from workflow-owned Bowtie2 index parameters
build and materialize reference and subtraction indexes through WorkflowCache