scanpy-qc-starter

name	scanpy-qc-starter
description	Use this skill to run a lightweight Scanpy QC pass on a toy count matrix with the repository-managed Scanpy environment.

Purpose

Provide a reproducible starting point for Scanpy-based QC work with toy matrix inputs, AnnData export, and a small verification report.

When to use

• You want to verify Scanpy and AnnData on this repository.
• You need a minimal example layout for single-cell QC work.

When not to use

• You need GPU-backed modeling or integrated single-cell workflows.

Inputs

• Tab-separated matrix with gene names in the first column and sample or cell columns after that

Outputs

• Summary statistics about matrix dimensions and zero fraction
• QC summary JSON with per-cell metrics
• Optional .h5ad artifact

Requirements

• slurm/envs/scanpy
• Run with slurm/envs/scanpy/bin/python

Procedure

1. Inspect examples/toy_counts.tsv.
2. Run python3 skills/transcriptomics/scanpy-qc-starter/scripts/preflight_counts.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv.
3. Run slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-qc-starter/scripts/run_scanpy_qc.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv --summary-out skills/transcriptomics/scanpy-qc-starter/assets/scanpy_qc_summary.json --h5ad-out scratch/scanpy/toy_counts_qc.h5ad.
4. Inspect total_counts, n_genes_by_counts, and pct_counts_mt in the summary output.

Validation

• Preflight script exits successfully.
• Reported dimensions match the example matrix.
• Scanpy writes a valid .h5ad file.
• QC summary includes per-cell metrics.

Failure modes and fixes

• Ragged rows: normalize the input to a rectangular TSV.
• Non-numeric counts: clean or coerce the count columns before QC.
• Missing Scanpy environment: recreate slurm/envs/scanpy and rerun with that interpreter.

Safety and limits

• This is a lightweight QC starter, not a full single-cell analysis workflow.
• Toy matrices are for environment verification and examples only.

Examples

• python3 .../preflight_counts.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv
• slurm/envs/scanpy/bin/python .../run_scanpy_qc.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv --summary-out scratch/scanpy/summary.json --h5ad-out scratch/scanpy/toy_counts.h5ad

Provenance

• Scanpy docs: https://scanpy.readthedocs.io/en/stable/
• Scanpy installation docs: https://scanpy.readthedocs.io/en/stable/installation.html
• Scanpy QC metrics API: https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.calculate_qc_metrics.html
• AnnData docs: https://anndata.readthedocs.io/en/latest/index.html
• scvi-tools docs: https://docs.scvi-tools.org/en/latest/index.html

Related skills

• snakemake-toy-workflow-starter