core_runtime

Core Runtime Scripts

This directory contains the active repo-owned runtime for the validated core workflow.

Purpose:

• keep the implemented core pipeline runnable without runtime dependence on upstream/source_scripts/
• preserve the validated RNA and DNA behavior in repo-owned code
• keep upstream/source_scripts/ only as provenance

The current core runtime set is:

• Tag.codon
• Tag_UMI.codon
• Tag_Lig3.codon
• Split_ReadsV2.codon
• FqToSAM.codon
• RNA_STARSOLO_ALIGN.sh
• RNA_FILTERED_BAM.sh
• RNA_COVERAGE.sh
• AlignDNA.sh
• utils.codon

Ownership rules:

• edits to files in this directory are pipeline changes and should be reviewed like any other repo code
• keep behavior aligned with the validated workflow unless a deliberate contract change is documented
• prefer targeted readability improvements over large rewrites of biological logic