Individual skill
nextflow
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.
backend/cli/skills/biology/nextflow/SKILL.md
Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 2, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 4,352
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- agent Repository topic
- ai Repository topic
- bun Repository topic
- cli Repository topic
- llm Repository topic
- ml Repository topic
- open-source Repository topic
- research Repository topic
- science Repository topic
- ai-agent Repository topic
- devops Derived category
- operations Derived category
- data Derived category
- testing Derived category
- research Derived category
- devops-containers Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 13,408 bytesSKILL.mdcore · 13,408 bytesSKILL.mdcore · 13,408 bytesSKILL.mdcore · 13,408 bytesSKILL.mdcore · 13,408 bytesreferences/configuration.mddoc · 11,318 bytesreferences/containers.mddoc · 4,598 bytesreferences/developing.mddoc · 15,378 bytesreferences/language.mddoc · 15,318 bytesreferences/nf-core-tools.mddoc · 6,357 bytesreferences/running-pipelines.mddoc · 6,806 bytesreferences/testing.mddoc · 6,744 bytes
Read excerpt
# Nextflow
## Overview
Nextflow is a workflow language and runtime for building **reproducible, portable, scalable** data pipelines. It is dominant in bioinformatics but works for any data-heavy computation. nf-core is a community curating production-grade Nextflow pipelines, reusable modules, and the `nf-core` tooling on top of Nextflow.
Key ideas:
- **Dataflow programming**: pipelines are `process` tasks connected by **channels**. Nextflow infers execution order and parallelism from data dependencies — there is no explicit scheduler to write.
- **Write once, run anywhere**: the same pipeline runs locally, on HPC (SLURM, SGE, LSF, PBS), and on cloud (AWS Batch, Google Batch, Azure Batch, Kubernetes) by changing config/profiles, not code.
- **Reproducibility**: per-task containers (Docker/Singularity/Apptainer/Conda/Wave) + `-resume` caching + pinned pipeline revisions.
- **DSL2** is the modern, required syntax: modular `process`/`workflow`/`include` definitions.
This skill covers both **running** existing pipelines and **developing** your own (Nextflow language + nf-core conventions, testing with nf-test, configuration, and deployment).
