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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.

80

Quality

100%

Does it follow best practices?

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Adds up to 20 points to the overall score

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

100%

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

The body is concise, actionable, and well-structured: executable verified commands, a sequenced workflow with validation and triage feedback loops, and a clean overview-plus-references layout. It respects token budget while giving Claude everything needed to operate.

DimensionReasoningScore

Conciseness

The body is lean and bullet-driven with no explanations of concepts Claude already knows (Nextflow, BAM, schedulers); every line directs action, matching the 'lean and efficient; every token earns its place' anchor.

3 / 3

Actionability

Provides two full, copy-paste-ready bash invocations whose flags (--tumor-bam, --genome, --profile, --executor slurm, --queue, --project, --cpus, --memory-gb, --walltime, --run, --dry-run) were verified to exist in scripts/run_pacsomatic.py, plus an executable test command.

3 / 3

Workflow Clarity

A clear numbered workflow with an explicit validation checkpoint (the --dry-run stop branch) and an error-recovery feedback loop ('If execution fails, report first failure point and next triage target (.nextflow.log, pipeline_info, failing task logs)').

3 / 3

Progressive Disclosure

SKILL.md is an overview pointing to well-signaled, one-level-deep references (agent-playbook.md, config-and-output.md, pacsomatic_guide.md, run_pacsomatic.py), all of which were verified to exist on disk; helper logic is appropriately split into the script rather than inlined.

3 / 3

Total

12

/

12

Passed

Description

100%

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 distinctive: it states concrete capabilities, gives explicit 'Use when/Triggers on' guidance, and occupies a clear niche unlikely to conflict with other skills. No vague fluff or over-claims are present.

DimensionReasoningScore

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'), matching the 'multiple specific concrete actions' anchor.

3 / 3

Completeness

Explicitly answers both what ('Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs') and when with a literal 'Use this skill when...' and 'Triggers on...' clause, not merely implied.

3 / 3

Trigger Term Quality

Natural user phrasings are covered ('run pacsomatic', 'prepare launch commands/scripts', 'perform dry-run checks', 'troubleshoot pipeline startup', named schedulers, 'tumor-normal workflows from BAM inputs'), giving good coverage of terms users would actually say.

3 / 3

Distinctiveness Conflict Risk

Targets a very specific niche (nf-core/pacsomatic matched tumor-normal from BAM) with named schedulers, making it clearly distinguishable and unlikely to trigger for the wrong skill.

3 / 3

Total

12

/

12

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.

Validation16 / 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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