nextflow

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.

Quality

93%

Does it follow best practices?

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Securityby

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Quality

Content

86%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, highly actionable skill body that keeps the SKILL.md as an overview while delegating depth to real reference files. It would tighten slightly by trimming background prose that restates general computing concepts.

Suggestions

Trim the 'Key ideas' bullets and Overview sentences that re-explain dataflow programming and write-once-run-anywhere — Nextflow-specific framing is useful, but the general concepts can be assumed.

Add an explicit failure/feedback loop for the 'debug a failed/-resume run' path (e.g., inspect `nextflow log`, identify the failed task, fix, re-run with `-resume`) to lift workflow clarity.

The 'Citing Scientific Agent Skills' section adds context-window cost unrelated to the user's task; consider moving citation guidance into a reference file.

Dimension	Reasoning	Score
Conciseness	Dense, high-value command tables and executable examples, but a few overview passages ('dominant in bioinformatics', re-explaining dataflow programming and write-once-run-anywhere) restate concepts Claude largely already knows.	4 / 5
Actionability	Copy-paste-ready `nextflow run` commands with pinned revisions and profiles, a complete runnable SAYHELLO pipeline, and full real CLI/nf-core tools command tables covering the common cases.	5 / 5
Workflow Clarity	A mode-routing decision table, numbered Quick Start steps, and the 'Always test first' verification checkpoint give a clear sequence; failure-recovery validation is mentioned but not fully sequenced into a feedback loop.	4 / 5
Progressive Disclosure	A clear overview routes to seven confirmed one-level-deep reference files, each named with a one-line description and surfaced through the 'Two Modes of Work' and 'Reference Files' sections.	5 / 5
	Total	18 / 20 Passed

Description

100%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: concrete capabilities, comprehensive trigger terms, explicit what/when guidance, and a distinctive niche. Every dimension hits the top anchor with no padding or over-claims.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Build, run, and debug', 'write or test a module/subworkflow with nf-test', 'configure executors/containers', 'scale a workflow', 'authoring nf-core-compliant pipelines' — covering the skill comprehensively.	5 / 5
Completeness	Explicitly answers both 'what' (Build, run, debug Nextflow pipelines and nf-core workflows end to end) and 'when' ('Use whenever the user mentions...') with concrete trigger phrases.	5 / 5
Trigger Term Quality	Comprehensive natural terms including the file extension (.nf), config file (nextflow.config), DSL2, processes/channels/operators, samplesheets, and all major container/executor/cloud synonyms a user would say.	5 / 5
Distinctiveness Conflict Risk	Clear niche (Nextflow/nf-core pipelines) with distinct, domain-specific triggers and minimal overlap with other skills; uses third-person voice throughout.	5 / 5
	Total	20 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/biology/nextflow/SKILL.md
Commit: 8d99f34

Reviewed: 9 days ago

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