Directory / Scientific Agent Skills (K-Dense) / pacsomatic

pacsomatic

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.
Description from the SKILL.md front matter.

Install

GitHub CLI v2.90+ (Copilot by default)

gh skill install K-Dense-AI/scientific-agent-skills pacsomatic

For Claude Code

gh skill install K-Dense-AI/scientific-agent-skills pacsomatic --agent claude-code

For Codex

gh skill install K-Dense-AI/scientific-agent-skills pacsomatic --agent codex

Commands follow each host's documentation (Any Agent Skills host (Claude Code, Codex, Cursor, Gemini CLI, Copilot…) docs). gh skill needs GitHub CLI 2.90 or later and is in public preview.

Listed from K-Dense Inc.'s catalog, not reviewed by us. Read the source before installing.

Catalog: Scientific Agent Skills (K-Dense)
Author: Beifang Niu
Source code: K-Dense-AI/scientific-agent-skills
License: MIT
Repository stars: 52,795 for K-Dense-AI/scientific-agent-skills (the whole catalog repo)
Version: 1.4
Added to catalog: Not tracked for this source
Last change: 2026-10-19 (last push to the repo)

What it contains

Skills: 1

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