scRNA-seq Pipeline Conventions

Use this skill for the scRNA-specific objects and deliverables shared by cellranger-multi-to-anndata, scrna-cxg-host, and consensus-nmf-multirun. Apply the CRAFT block and analysis-code-conventions for stage naming, layout, helper boundaries, configuration placement, and generic restartability.

Routing decision tree

What scRNA deliverable decision is being made?
│
├─ Is this an intermediate checkpoint or a finalized object?
│     → checkpoints-and-objects.md
│
├─ Which gene identifier should be active at delivery?
│     → gene-identifier-packaging.md
│
├─ Which embeddings must the packaged object carry?
│     → embedding-deliverables.md
│
└─ How should obs metadata and uncertain labels be packaged?
      → metadata-packaging.md

Routing contract

1. Apply the repository's rendered CRAFT block for standing stage and result mechanics; load analysis-code-conventions for structural judgment.
2. Select the scRNA deliverable question and read its reference completely.
3. Load every relevant reference when finalizing an object because identifier, embedding, metadata, and derivation guarantees interact.
4. Read numeric thresholds and project choices from the project's current configuration and decision records. Preserve their provenance.
5. Use the adjacent conversion or hosting skill for tool-specific execution.

References (load on demand)

Intent	Load
Plan recovery objects and the canonical milestone	references/checkpoints-and-objects.md
Package symbols while preserving stable identifiers	references/gene-identifier-packaging.md
Carry discovery and integrated embeddings	references/embedding-deliverables.md
Clean obs and preserve annotation uncertainty	references/metadata-packaging.md

Adjacent skills

• analysis-code-conventions — structural stages, helpers, configuration, and restartable data flow.
• cellranger-multi-to-anndata — build the initial pooled AnnData object.
• single-cell-rna-qc — perform assay QC before milestone packaging.
• anndatar-seurat-scanpy-conversion — derive a Seurat object from AnnData.
• louper-seurat-conversion — derive a Loupe object from the packaged data.
• scrna-cxg-host — validate and host the CellxGene derivative.

When not to use

• Generic stage sequencing, helper extraction, or project layout decisions.
• Assay methodology such as QC models, integration choice, or differential tests.
• Throwaway exploration with no durable scRNA object or collaborator handoff.