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nextflow

70 / 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 hashgraph-online/awesome-codex-plugins (GitHub) · coding · 1,568 stars · scanned at commit 3e1e6b2

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or de…

Works with any agent that supports SKILL.md skills.

What this skill can do

Safer alternatives

Low-risk skills in the same category (coding) that look related. Check that one does what you need.

• 100 Low risknextflow-pipeline-executora5c-ai/babysitter · 1,903 stars

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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/hashgraph-online/awesome-codex-plugins' "$d" && git -C "$d" checkout --quiet '3e1e6b20ffc28f42923e391f29f075c424e19e64' -- 'plugins/KalarisLabs/research-agent-skills/skills/nextflow' && mkdir -p ~/.agents/skills && cp -R "$d"/'plugins/KalarisLabs/research-agent-skills/skills/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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