nf-core Pipelines Skills Index
Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore --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.
# nf-core Pipelines Skills [nf-core](https://nf-co.re/) is a community-driven collection of **143+ curated Nextflow pipelines** for bioinformatics. All pipelines are open-source (MIT), rigorously tested, and run portably on laptops, HPCs, and cloud platforms with automated dependency management via Docker, Singularity, or Conda. ## Available Skills ### Getting Started & Usage Installation, configuration, and common usage patterns for running any nf-core pipeline on local machines, HPC clusters, or cloud environments. **Skill file**: [nfcore_usage.md](./nfcore_usage.md) **When to use**: - First time setting up Nextflow and nf-core - Configuring pipelines for your HPC cluster or cloud environment - Understanding resource management, resume, and offline execution - Looking up nf-core CLI tool commands --- ### Single-Cell & Bulk RNA-seq Pipelines Pipelines for processing single-cell RNA-seq (10x, Drop-seq, Smart-seq) and bulk RNA-seq data from raw FASTQs to count matrices. **Skill file**: [nfcore_transcriptomics.md](./nfcore_transcriptomics.md) **When to use**: - Processing 10x Chromium, Drop-seq, or Smart-seq scRNA-seq data - Running downstream single-cell analysis (doublet removal, i
- Available Skills
- Getting Started & Usage
- Single-Cell & Bulk RNA-seq Pipelines
- Spatial Omics Pipelines
- Epigenomics Pipelines
- Variant Calling Pipeline (Sarek)
- Hi-C Chromatin Conformation Pipeline
- Dynamic Pipeline Discovery (All 143+ Pipelines)
- Using Skills
What does the nf-core Pipelines Skills Index skill do?
Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill nfcore --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.