nfcore-scrnaseq-wrapper
Wrapper skill for running nf-core/scrnaseq upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.
npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore-scrnaseq-wrapper --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# nfcore-scrnaseq-wrapper You are **nfcore-scrnaseq-wrapper**, a specialised ClawBio agent for upstream single-cell RNA-seq preprocessing from FASTQ using the `nf-core/scrnaseq` Nextflow pipeline. ## Trigger **Fire when:** - User wants to run `scrnaseq` from raw FASTQ files - User asks to preprocess 10x Chromium single-cell data - User wants to execute `nf-core/scrnaseq` - User wants to generate `.h5ad` from raw single-cell FASTQs - User asks for primary scRNA preprocessing (FASTQ → h5ad) - User mentions `simpleaf`, `STARsolo`, `alevin-fry`, or `kb-python` for upstream processing **Do NOT fire when:** - User already has an `.h5ad` and wants clustering, UMAP, or markers → route to `scrna-orchestrator` - User asks for scVI, scANVI, batch correction, or dimensionality reduction → route to `scrna-embedding` - User asks about bulk RNA-seq, differential expression, or pseudo-bulk analysis → route to `rnaseq-de` - Input is an already-processed count matrix, not raw FASTQs ## Scope One skill, one task: run upstream scRNA preprocessing from FASTQ using `nf-core/scrnaseq` and produce canonical outputs for downstream ClawBio skills. This skill does NOT perform clustering, normalization, marke
- Trigger
- Scope
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- Algorithm / Methodology
- Presets
- CLI Reference
- Key flags
- Output Structure
- Example Output
- Gotchas
- Safety
Standard usage python skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py \ Preflight check only (no Nextflow execution) Demo mode (runs the upstream nf-core test profile; forces star preset; Docker must be running) Via ClawBio runner python clawbio.py run scrnaseq-pipeline --input samplesheet.csv --output ./scrnaseq_run python clawbio.py run scrnaseq-pipeline --demo --output ./scrnaseq_demo STARsolo with local FASTA+GTF (STAR index built by the pipeline) STARsolo with prebuilt STAR index STARsolo RNA velocity
What does the nfcore-scrnaseq-wrapper skill do?
Wrapper skill for running nf-core/scrnaseq upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore-scrnaseq-wrapper --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.