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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.

75

Quality

94%

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SKILL.md
Quality
Evals
Security

Quality

Content

92%Weight 40%Scale 1-5

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

A lean, highly actionable body: every step carries skill-specific contract knowledge rather than generic explanation, examples are executable, and validation/triage checkpoints are explicit. The only meaningful improvement is moving the duplicated upstream provenance detail into the reference guide.

DimensionReasoningScore

Conciseness

The body is dense with helper-specific operational contracts Claude would not know (dry-run scope limits, launcher scheduler vs process.executor, params-file precedence, walltime normalization) with zero concept padding. Minor trim opportunities remain: the upstream release/tag provenance paragraph in 'When to use' largely duplicates references/pacsomatic_guide.md, fitting the 'minor instances of over-explanation that could be trimmed' anchor.

4 / 5

Actionability

The dry-run example is a complete copy-paste-ready command with every flag shown, the Slurm follow-up gives exact additional options with assembly instructions, and verification is concretely executable ('uv run skills-ref validate skills/pacsomatic', 'python tests/run_all.py --isolated pacsomatic'). Specific rules like 'normalizes 48:00 to Slurm 48:00:00' and 'keep paths absolute because the launcher cwd is the outdir' cover the common cases fully.

5 / 5

Workflow Clarity

The 7-step workflow has an explicit validation checkpoint (step 3 --dry-run with its scope limits stated), an explicit review gate before execution (step 4), execution gating ('Use --run only for requested execution'), and error-recovery guidance (failure-triage next step, keeping work/cache state stable for --resume). Validation, review, and feedback loops are all explicit rather than implicit.

5 / 5

Progressive Disclosure

The body is a genuine overview: three real one-level-deep reference files (all verified to exist, containing only external URLs rather than nested local references), each linked inline at the point of need and listed with labels in 'Verification and references', plus the script in scripts/. Content is appropriately split between SKILL.md, references, and the script.

5 / 5

Total

19

/

20

Passed

Description

92%Weight 40%Scale 1-5

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

An exemplary description: third-person voice, concrete multi-action capability list, an explicit 'Use for' trigger clause, and active exclusion of the most confusable adjacent domains. The only gap is modest synonym coverage (long-read, SMRT) for trigger terms.

DimensionReasoningScore

Specificity

Enumerates multiple concrete actions spanning the skill's full scope: 'Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows', 'samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting'. This matches the comprehensive multi-action anchor, not the 'several specific actions with minor gaps' anchor.

5 / 5

Completeness

Clearly answers both: 'what' via two sentences of concrete capabilities and 'when' via the explicit trigger clause 'Use for pacsomatic run preparation and execution'. The added negative boundary ('not general short-read somatic analysis or medical imaging PACS') further sharpens the trigger, matching the top anchor.

5 / 5

Trigger Term Quality

Good natural keyword coverage: 'pacsomatic', 'PacBio HiFi', 'tumor-normal', 'unaligned BAM', 'Nextflow', 'samplesheet', and all four scheduler names a user would actually say. Falls short of the 5 anchor because common synonyms like 'long-read', 'SMRT', or the '.bam' extension form are absent, though it does include 'somatic' via the exclusion clause.

4 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (nf-core/pacsomatic, matched PacBio HiFi tumor-normal) and explicitly disambiguates the two most likely wrong-trigger candidates: 'not general short-read somatic analysis or medical imaging PACS'. Minimal conflict risk with any other skill.

5 / 5

Total

19

/

20

Passed

Validation

100%

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
Reviewed

Table of Contents

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