pacsomatic

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

Quality

83%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

Quality

Content

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Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is well-structured, actionable, and sequenced with validation built into the workflow, leaning on a single helper entrypoint and real reference files. Minor improvements are available in deduplicating triggers, adding executor-specific examples, and annotating the reference list.

Suggestions

Remove the 'When to Use' trigger-phrase list or shrink it, since the same triggers already appear in the frontmatter description, to recover token budget.

Annotate each entry in the References section with what it contains (e.g., 'pacsomatic_guide.md — pipeline parameters and output structure') so navigation is unambiguous.

Add an explicit validate->fix->retry feedback loop in the Workflow (e.g., 'if --dry-run validation fails, report the failing constraint and re-run after correction') to strengthen the validation checkpoint.

Dimension	Reasoning	Score
Conciseness	The body is lean and assumes Claude's competence (no explanation of Nextflow/BAM basics), but the 'When to Use' trigger list duplicates the frontmatter and the 'Agent Response Contract' is slightly padded, so a few tokens could be trimmed.	4 / 5
Actionability	Provides copy-paste-ready bash commands covering dry-run and Slurm execution plus explicit routing rules and a concrete inputs list; minor gaps remain (no LSF/PBS/SGE executor examples shown), keeping it just below fully comprehensive.	4 / 5
Workflow Clarity	An 8-step numbered workflow is clearly sequenced with a dry-run validation checkpoint (step 6) and triage guidance for failures, but the validate->fix->retry feedback loop is implicit rather than spelled out.	4 / 5
Progressive Disclosure	Well-organized sections (Quick Start, Inputs, Workflow) with real one-level-deep references listed at the end; the references are present and valid but not annotated with what each file contains, a minor navigation gap.	4 / 5
	Total	16 / 20 Passed

Description

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Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is specific, complete, and clearly niched, explicitly stating both capabilities and concrete trigger conditions in third person. Trigger-term coverage is strong though not exhaustive of every synonym.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures' — with comprehensive coverage of the toolkit's capabilities.	5 / 5
Completeness	Explicitly answers both 'what' (operator toolkit for matched tumor-normal workflows from BAM inputs with the listed actions) and 'when' ('Use this skill when the user needs to...' plus 'Triggers on requests to...') with concrete trigger phrases.	5 / 5
Trigger Term Quality	Includes natural phrases users would say ('run pacsomatic', 'prepare launch commands/scripts', 'dry-run checks', 'troubleshoot pipeline startup') plus scheduler names, but a few common synonyms/extensions are absent, keeping it just below comprehensive.	4 / 5
Distinctiveness Conflict Risk	Targets a clear niche — nf-core/pacsomatic matched tumor-normal analysis from BAMs — with distinct pipeline-specific triggers, giving minimal overlap risk with other skills.	5 / 5
	Total	19 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/pacsomatic/SKILL.md
Commit: 36d8f13

Reviewed: about 7 hours ago

Table of Contents

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