[SonderXiaoming]

SMARTer smRNA libraries need protocol-specific trimming and must bypass the Total RNA UMI workflow. This change adds a selectable smRNA profile while preserving smarter_total_rna as the default, and produces a separate concise RNA-seq summary alongside the comprehensive report.

Changes

• Add --kit smarter_smrna for single-end R1 or paired-end R1/R2 input, with sense/forward orientation by default, structure/poly(A) trimming, Q20 filtering, and no UMI extraction or deduplication.
• Make STAR profiles configurable through Bash arrays; route downstream QC, expression, circRNA inputs, coverage, and reporting through the selected profile. Retain chimeric output and disable biological poly(A)-tail detection for smRNA libraries.
• Include kit/effective strand in step metadata and reject incompatible cross-kit resume attempts. Document that v1.0 output signatures require regeneration.
• Generate a standalone Step 27 summary of read retention, mapping, genomic regions, orientation, and top genes; support gene-only expression matrices when circRNA results are absent.
• Update README, release manifest, and checksums. Normalize text to LF for reproducible hashes across platforms.