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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.

70

Quality

88%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is pacsomatic in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

81%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 well-structured operational skill: executable commands, a sequenced workflow with explicit validation and failure-triage targets, and a genuine reference bundle. The main defects are two commands pointing at non-existent files (config.yaml, tests/pacsomatic), an unlabeled references list, and some duplication between the When-to-Use/Routing and frontmatter/Workflow sections.

Suggestions

Fix or remove the non-existent paths: either add a config.yaml baseline and tests/pacsomatic suite to the bundle, or drop the 'Configuration' and 'Testing' sections — as written they direct the agent to files that do not exist.

Label the References entries with what each file contains and link them from the relevant sections (e.g. 'Executor/CLI options: see references/config-and-output.md'), matching the well-signaled one-level-deep pattern.

Tighten conciseness by trimming the 'When to Use This Skill' trigger-phrase list (duplicated from the frontmatter description) and merging overlapping rules from 'Routing and Execution Rules' into the 'Workflow' section.

DimensionReasoningScore

Conciseness

The body is efficient and assumes Claude's competence (no concept explanations, tight bullet lists, executable Quick Start commands), but has some redundancy: "When to Use This Skill" restates trigger phrases already in the frontmatter, and "Routing and Execution Rules" overlaps the "Workflow" section. This is 'minor instances of over-explanation that could be trimmed' (level 4) rather than the fully lean level-5 anchor, and clearly above the noticeably-verbose level-3 anchor.

4 / 5

Actionability

The core path is fully executable — copy-paste-ready Quick Start commands with real flags for both dry-run and Slurm execution, plus a concrete routing table. However, two commands point at files that do not exist in the bundle: "Use `config.yaml` as the baseline" (no config.yaml present) and "python -m unittest discover -s tests/pacsomatic -v" (no tests directory). These are peripheral rather than key details, placing it at level 4 ('concrete commands with minor gaps') rather than level 5, and well above the incomplete level-3 anchor.

4 / 5

Workflow Clarity

The 8-step "Workflow" is clearly sequenced with validation explicit and up front (steps 1–3 validate identity, paths, and runtime), a dry-run stop checkpoint ("If `--dry-run` and not `--run`, stop after artifact generation"), and error-recovery guidance ("If execution fails, report first failure point and next triage target (`.nextflow.log`, `pipeline_info`, failing task logs)"). This matches the level-5 anchor: explicit validation steps plus feedback loops for error recovery.

5 / 5

Progressive Disclosure

The body is a well-structured overview with a References section listing real one-level-deep bundle files (references/agent-playbook.md, references/config-and-output.md, references/pacsomatic_guide.md, scripts/run_pacsomatic.py — all verified to exist). Gaps keep it at level 4 rather than 5: the reference entries are a bare unlabeled list with no per-file description or linkage from the relevant sections, and two referenced paths (config.yaml, tests/pacsomatic) do not exist in the bundle. It is clearly better organized than the level-3 anchor's inlined-should-be-separate content.

4 / 5

Total

17

/

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.

A strong description: concrete, comprehensive action list tied to a specific named pipeline, with explicit 'Use when' and 'Triggers on' clauses in third-person voice. The only weakness is modest keyword coverage — a few natural synonyms (PacBio/HiFi, .bam) are absent.

DimensionReasoningScore

Specificity

The description 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" — covering the skill's operations comprehensively, which matches the level-5 anchor rather than the level-4 anchor with 'minor gaps in coverage'.

5 / 5

Completeness

It explicitly answers both questions: 'what' ("Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs... generate pacsomatic-compliant samplesheets, prepare... launch artifacts") and 'when' with concrete trigger guidance ("Use this skill when the user needs to..." and "Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot..."). This matches the level-5 anchor exactly.

5 / 5

Trigger Term Quality

Natural trigger phrasing is good ("run pacsomatic", "dry-run checks", "troubleshoot pipeline startup and scheduler submission errors", scheduler names, "tumor-normal", "BAM"), but a few natural terms users might say are missing, such as PacBio/HiFi and the .bam file extension. It sits above the level-3 anchor ('missing common variations or synonyms' applies only to a few terms) but below the comprehensive-with-synonyms level-5 anchor.

4 / 5

Distinctiveness Conflict Risk

The description repeatedly pins the exact pipeline ("nf-core/pacsomatic") with domain-specific triggers (tumor-normal, samplesheets, LSF/Slurm/PBS/SGE submission), giving it a clear niche with minimal conflict risk against other skills. It is not merely 'mostly distinct' as in the level-4 anchor; the named pipeline makes triggering for the wrong skill unlikely.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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