Codex/python conversion#10

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byee4 wants to merge 10 commits into

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codex/python-conversion

Commits on Mar 19, 2026

Step 1: document CWL pipeline, Perl script contracts, and output formats
Brian Yee
committed
Step 2: inventory PPA1 inputs and generate expected-output manifest
Brian Yee
committed
Step 3: add deterministic mini fixtures and checksum-based validation
Brian Yee
committed
Step 4a: convert split/merge Perl utilities to Python with parity tests
Brian Yee
committed
Step 4b: add Python compatibility shims for parser/dedup Perl scripts
Brian Yee
committed
Step 5a: add Snakemake SE foundation with split/merge parity validation
Brian Yee
committed
Enforce Python+Snakemake-only branch structure
Brian Yee
committed
Implement native SE parser in Python and align config keys to CWL schema
Brian Yee
committed
Support CWL-style YAML job input in Snakemake config
Brian Yee
committed
Merge pull request #9 from YeoLab/codex/python-conversion-python-only-cleanup
byee4
authored