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Build, run, and debug Nextflow data pipelines and nf-core workflows end to end.
Passed 22 of 22 test cases with the skill, and 17 of 22 without it.
and 3 more in the full report
5 fixed17 passed either way0 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
A pipeline developer wants to update `nextflow_schema.json` to add parameter validation rules, default values, and help text for pipeline CLI flags. Which command in `nf-core` CLI launches the schema builder GUI?
| Checked | Without skill | With skill |
|---|---|---|
| Recommends running `nf-core pipelines schema build` to open the interactive schema editor. | Missed | Passed |
The instructions your model reads when the skill loads.
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:
process tasks connected by channels. Nextflow infers execution order and parallelism from data dependencies — there is no explicit scheduler to write.-resume is a computational cache, not scientific validation. Conda is an environment manager; Wave resolves/builds images rather than executing them.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).
Use this skill when the user wants to:
.nf scripts, nextflow.config, profiles, or nextflow_schema.json.main.nf, meta.yml, tests/, nf-test).take/emit, publishDir, ext.args, meta maps.This review targets stable Nextflow 26.04.6, nf-core tools 4.1.0, and nf-test 0.9.5. Nextflow needs Bash 3.2+ and Java 17–26; verify java -version (a launcher on PATH does not prove a runtime is installed). The strict parser is the default in 26.04. See release notes and the 26.04 migration guide. Stable and edge documentation can differ; do not use a preview feature without its version/flag.
# Install Nextflow (self-installing launcher)
export NXF_VER=26.04.6
curl -fsSL https://get.nextflow.io -o install-nextflow.sh
# Review the installer before executing it.
bash < install-nextflow.sh
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin/"
export PATH="$HOME/.local/bin:$PATH"
nextflow info # verify
# Alternative (illustrative; confirm package availability and Java compatibility)
test cases passed, vs 17 / 22 without
More skills from the same source and nearby in the registry, with their headline benchmark lift.