PlantAI-dev/.planning/rnaseq_samples_authority/task_plan.md

RNA-seq samples.yaml authority planning

Goal

Produce a reviewed, implementation-ready revision plan that makes the user-confirmed input/samples.yaml the execution authority for R1/R2 paths, with fastq_1/fastq_2 mapped once to canonical r1/r2 and no filename-based execution gate.

Assumptions

• Scope is paired-end RNA-seq with one R1 and one R2 file per sample for this revision.
• Frontend review rows keep fastq_1 and fastq_2.
• Confirmed YAML keeps the existing canonical samples.<sample_id>.r1/r2 contract.
• Filename heuristics remain only for generating a draft.

Phases

• [complete] Phase 0: documentation and code-path discovery
• [complete] Phase 1: affected-layer and contract analysis
• [complete] Phase 2: draft surgical revision design and validation matrix
• [in_progress] Phase 3: adversarial plan review and revisions
• [pending] Phase 4: publish final implementation plan

Success criteria

• Every production filename-based RNA-seq readiness gate is identified.
• Every production RNA-seq branch that can select an arbitrary YAML instead of the confirmed sample config is identified.
• The plan names exact functions/files to change and exact behaviors to preserve.
• Draft versus confirmed configuration is unambiguous.
• Unit, API, and subset end-to-end validation cover arbitrary FASTQ names.
• No implementation code is changed during planning.

Errors encountered

• The previously known Codex binary path under .nvm/versions/node/v22.22.0 no longer exists; resolved the active binary with command -v codex as /home/xia-lab/.npm-global/bin/codex.