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nextflow-hello-workflow

95 / 100 · Low risk

Fine to try.

By ma-compbio-lab/SkillFoundry (GitHub) · productivity · 44 stars · scanned at commit 4a8cc0c

Use this skill to run a minimal Nextflow workflow through the repo-managed Java and Nextflow prefix, either locally or on the Slurm cluster. Do not use it for containerized production pipelines.

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

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

if [ -e ~/.agents/skills/'nextflow-hello-workflow' ] || [ -L ~/.agents/skills/'nextflow-hello-workflow' ]; then echo 'A skill folder named nextflow-hello-workflow already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/ma-compbio-lab/SkillFoundry' "$d" && git -C "$d" checkout --quiet '4a8cc0cd9f923cde47a7f542d4a84b92bbabc59f' -- 'skills/reproducible-workflows/nextflow-hello-workflow' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/reproducible-workflows/nextflow-hello-workflow' ~/.agents/skills/'nextflow-hello-workflow' && 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-hello-workflow' ~/.claude/skills/'nextflow-hello-workflow' (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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