Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill pacsomaticnpx skills add K-Dense-AI/scientific-agent-skills --skill pacsomatic -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill pacsomatic -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/pacsomaticgh skill install K-Dense-AI/scientific-agent-skills pacsomaticgit 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/pacsomatic ~/.claude/skills/pacsomatic # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/pacsomatic ~/.agents/skills/pacsomatic # Codex, Cursor, Gemini CLI, Copilot, OpenCode