nextflow
Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows
by k-dense-aiFree
Description
nextflow is an agent skill for building, running and debugging Nextflow DSL2 pipelines and nf-core workflows. Nextflow is a workflow language and runtime for reproducible, portable and scalable data pipelines, and it is widely used in bioinformatics, though it works for any data-heavy computation. nf-core is a community that curates production-grade Nextflow pipelines, reusable modules and tooling. The skill explains the key ideas. Pipelines are made of processes connected by channels, and Nextflow works out the execution order and parallelism from the data dependencies. The same pipeline can run on a laptop, on HPC schedulers such as SLURM, SGE, LSF and PBS, or on cloud batch services and Kubernetes, by changing configuration profiles rather than code. Reproducibility comes from pinned software environments, pinned pipeline revisions, and recorded parameters. The skill is clear that resuming a run is a computational cache rather than scientific validation, and that Conda is an environment manager while Wave builds images. DSL2 is the required syntax.…
Highlights
- Nextflow DSL2 pipelines
- nf-core conventions and modules
- Runs on laptops, HPC and cloud
- Profiles for portability
- nf-test testing and deployment
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nextflow FAQ
What is Nextflow?
A workflow language and runtime for reproducible, portable and scalable data pipelines, widely used in bioinformatics.
What is nf-core?
A community that curates production-grade Nextflow pipelines and reusable modules.
Can the same pipeline run on different systems?
Yes. The skill says it can run locally, on HPC schedulers and on cloud services by changing profiles, not code.
Does resuming a run prove results are correct?
No. The skill says resume is a computational cache, not scientific validation.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill nextflow.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best nextflow alternatives?
Popular alternatives to nextflow include latchbio-integration, pacsomatic and dnanexus-integration. See all nextflow alternatives