nextflow

89 / 100 · Low risk

Fine to try. Some of what it can do is expected: a devops skill usually runs commands, installs tools and uses cloud credentials.

By boisenoise/skills-collections (GitHub) · devops · 12 stars · scanned at commit 419c39f

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README. Expected for a devops skill.

Found in 4 places.

skills/kdense-nextflow/SKILL.md, line 43export NXF_VER=26.04.6
skills/kdense-nextflow/SKILL.md, line 58uv tool install "nf-core==4.1.0"
skills/kdense-nextflow/SKILL.md, line 83nextflow run nf-core/rnaseq -r 3.27.0 -profile test,docker --outdir test_results

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skills/kdense-nextflow/SKILL.md, line 129nextflow run main.nf # add -resume on reruns

Sends data to these websites: get.nextflow.io, get.nf-test.com

This is disclosed by the author in the skill's SKILL.md or README. Expected for a devops skill.

Found in 2 places.

skills/kdense-nextflow/SKILL.md, line 44curl -fsSL https://get.nextflow.io -o install-nextflow.sh
skills/kdense-nextflow/references/testing.md, line 27curl -fsSL https://get.nf-test.com -o install-nf-test.sh

Changes files outside its own folder

This is disclosed by the author in the skill's SKILL.md or README.

Found in 4 places.

skills/kdense-nextflow/SKILL.md, line 47mkdir -p "$HOME/.local/bin"
skills/kdense-nextflow/SKILL.md, line 48mv nextflow "$HOME/.local/bin/"
skills/kdense-nextflow/references/testing.md, line 30mkdir -p "$HOME/.local/bin"

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skills/kdense-nextflow/references/testing.md, line 31mv nf-test "$HOME/.local/bin/"

Install

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

if [ -e ~/.agents/skills/'nextflow' ] || [ -L ~/.agents/skills/'nextflow' ]; then echo 'A skill folder named nextflow already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/boisenoise/skills-collections' "$d" && git -C "$d" checkout --quiet '419c39fde874b8baecbb36a397b967e0190a2ece' -- 'skills/kdense-nextflow' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/kdense-nextflow' ~/.agents/skills/'nextflow' && 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' ~/.claude/skills/'nextflow' (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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Score history

Date	Version	Score
2026-11-12	`419c39f`	89
2026-11-08	`5fe45e5`	89
2026-11-06	`b89b2f5`	89

Also found in

Identical copies of this skill exist at:

LeoYeAI/agent-master-skills/skills/nextflow