Agent skill · research science · anthropics
nextflow-development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
Why this skill is useful
Provides specific commands and workflows for running nf-core bioinformatics pipelines that the AI wouldn't reliably generate on its own.
What it needs
Requires docker, nextflow, openjdk-11 installed locally. About 4k tokens when loaded. Last updated 2026-08-07. 23,345 stars on the source repository.
What this skill does
nf-core Pipeline Deployment Run nf-core bioinformatics pipelines on local or public sequencing data. Target users: Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis. Workflow Checklist --- Step 0: Acquire Data (GEO/SRA Only) Skip this step if user has local FASTQ files. For public datasets, fetch from GEO/SRA first. See references/geo-sra-acquisition.md for the full workflow. Quick start: DECISION POINT: After fetching study info, confirm with user: Which sample subset to download (if multiple data types) Suggested genome and pipeline Then continue to Step 1. --- Step 1: Environment Check Run first. Pipeline will fail without passing environment. All critical checks must pass. If any fail, provide fix instructions: Docker issues Problem Fix --------- ----- Not installed Install from https://docs.docker.com/get-docker/ Permission denied sudo usermod -aG docker $USER then re-login Daemon not running sudo systemctl start docker Nextflow issues Problem Fix --------- ----- Not installed curl -s https://get.nextflow.io \ bash && mv nextflow ~/bin/ Version < 23.04 nextflow self-update Java issues Problem Fix --------- ----- Not installed / < 11 sudo apt install openjdk-11-jdk Do not proceed until all checks pass. For HPC/Singularity, see references/troubleshooting.md. --- Step 2: Select Pipeline DECISION POINT: Confirm with user before proceeding. Data Type Pipeline Version Goal ----------- ---------- --------- ------ RNA-seq rnaseq 3.22.2 Gene expression WGS/WES sarek 3.7.1 Variant calling ATAC-seq atacseq 2.1.2 Chromatin accessibility Auto-detect from data: For pipeline-specific details: references/pipelines/rnaseq.md references/pipelines/sarek.md references/pipelines/atacseq.md --- Step 3: Run Test Profile Validates environment with small data. MUST pass before real data. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills anthropics/nextflow-development