Add serial alignment preprocessing for contamination removal

## Summary Implement PEPPRO's serial alignment strategy to efficiently remove rDNA, mtDNA, and decoy sequences before primary alignment. ## Features to implement - Sequential alignment to rDNA → mtDNA → user-defined decoys → primary genome - Configurable decoy sequence support - Alignment statistics tracking for each step - Memory and speed optimization through read reduction ## Implementation details - Create subworkflow: subworkflows/local/serial_alignment - Add bowtie2 serial alignment modules - Implement alignment statistics collection - Add configurable decoy genome support via params ## Technical specifications - Use bowtie2 parameters: -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 for serial alignments - Primary alignment with --very-sensitive - Report alignment rates and read counts at each step ## Acceptance criteria - [ ] Functional serial alignment subworkflow - [ ] 30-40% processing time reduction on test datasets - [ ] Comprehensive alignment statistics output - [ ] Support for custom decoy genomes - [ ] Maintained alignment quality vs direct alignment ## References - PEPPRO serial alignment implementation