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nextflow-workflow-engine

79 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb

Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.

Works with any agent that supports SKILL.md skills.

What this skill can do

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Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'nextflow-workflow-engine' ] || [ -L ~/.agents/skills/'nextflow-workflow-engine' ]; then echo 'A skill folder named nextflow-workflow-engine already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/scientific-computing/nextflow-workflow-engine' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/scientific-computing/nextflow-workflow-engine' ~/.agents/skills/'nextflow-workflow-engine' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'nextflow-workflow-engine' ~/.claude/skills/'nextflow-workflow-engine' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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