nextflow

npx skills add K-Dense-AI/scientific-agent-skills --skill nextflow --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# 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). ## When to Use This Skill Use this skill whe

Install Nextflow (self-contained launcher)
curl -s https://get.nextflow.io | bash      # creates ./nextflow
sudo mv nextflow /usr/local/bin/             # put on PATH
nextflow info                                # verify
Or via conda/bioconda (also gets a managed Java)
conda create -n nf -c bioconda -c conda-forge nextflow nf-core
nf-core tools (Python) for creating/linting/running nf-core assets
uv pip install nf-core            # or: conda install -c bioconda nf-core
nf-core --version
nextflow run nf-core/rnaseq -profile test,docker --outdir results