nfcore-rnaseq-wrapper
Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.
npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore-rnaseq-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-rnaseq-wrapper You are **nfcore-rnaseq-wrapper**, a specialised ClawBio agent for upstream bulk RNA-seq preprocessing from FASTQ or BAM inputs using `nf-core/rnaseq`. ## Trigger **Fire when:** - User wants to run `nf-core/rnaseq` - User asks for bulk RNA-seq preprocessing from raw FASTQ files - User wants FASTQ to gene-count matrix, Salmon counts, RSEM counts, or MultiQC outputs - User mentions STAR/Salmon, STAR/RSEM, HISAT2, or Bowtie2/Salmon as upstream bulk RNA-seq routes - User asks for a reproducible Nextflow wrapper before downstream differential expression **Do NOT fire when:** - User already has a count matrix and wants differential expression -> route to `rnaseq-de` - User has single-cell FASTQs or wants `.h5ad` -> route to `nfcore-scrnaseq-wrapper` - User wants clustering, marker genes, or Scanpy analysis -> route to `scrna-orchestrator` - Input is clinical DNA/VCF data rather than RNA-seq reads ## Scope One skill, one task: run upstream bulk RNA-seq preprocessing through `nf-core/rnaseq` and produce count-matrix handoff artifacts for downstream ClawBio skills. This skill does not perform differential expression. It emits a prefilled `rnaseq-de` command templa
- Trigger
- Scope
- Why This Exists
- Core Capabilities
- Aligners
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
Preflight only; no Nextflow execution python clawbio.py run rnaseq-pipeline \ Demo mode using upstream test profile python clawbio.py run rnaseq-pipeline --demo --output ./rnaseq_demo STAR + Salmon default route Explicit FASTA/GTF reference RSEM route Contaminant screening with Kraken2 + Bracken Auto-handoff to rnaseq-de when all flags are provided Prokaryotic transcriptomes via Bowtie2+Salmon
What does the nfcore-rnaseq-wrapper skill do?
Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore-rnaseq-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.