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.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill nextflownpx skills add K-Dense-AI/scientific-agent-skills --skill nextflow -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill nextflow -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/nextflowgh skill install K-Dense-AI/scientific-agent-skills nextflowgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/nextflow ~/.claude/skills/nextflow # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/nextflow ~/.agents/skills/nextflow # Codex, Cursor, Gemini CLI, Copilot, OpenCode