Nextflow
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end.
Install
npx skills add synthetic-sciences/openscience --skill nextflow -g -a claude-code -y- Repository
- synthetic-sciences/openscience4.3k
- Category
- Testing
- Updated
- 5d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 3,000 tokens
- Runs scripts
- No, instructions only
What it does
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.
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
processtasks 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) +
-resumecaching + pinned pipeline revisions. - DSL2 is the modern, required syntax: modular
process/workflow/includedefinitions.
This skill covers both running existing pipelines and developing your own (Nextflow language + nf-core conventions, testing with nf-test, configuration, and deployment).
When to Use This Skill
Use this skill when the user wants to:
- Run an nf-core or custom Nextflow pipeline, or debug a failing/resuming run.
- Write or modify
.nfscripts,nextflow.config, profiles, ornextflow_schema.json. - Author or test nf-core-style modules/subworkflows (
main.nf,meta.yml,tests/, nf-test). - Configure executors, containers, or resources; scale to HPC or cloud.
- Build a reproducible scientific/bioinformatics workflow (even if "Nextflow" is not named).
- Understand processes, channels, operators,
take/emit,publishDir,ext.args, meta maps.
Setup
Nextflow needs Bash and Java 17 or newer (17, 25 supported). Verify with java -version.
