Developer tool
Nextflow agent skills for Claude Code, Codex and other agents.
- skills
- 27
- Type
- Developer tool
- Website
- nextflow.io
- Official GitHub
- nextflow-io
- Reviews
- See Nextflow on Enlisted
Nextflow skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. | bactopia/ | 522 | — | ~4.1k | Automated safety check: Pass | MIT | 2 mo ago |
| 2 | Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia… | bactopia/ | 522 | — | ~1.3k | Automated safety check: Pass | MIT | 2 mo ago |
| 3 | Cut a new tagged release of the dockstore/dockstore webservice (alpha/beta/rc/stable/hotfix), following the dockstore-deploy wiki's Hubflow + Maven CI-friendly-versions process. | dockstore/ | 131 | — | ~2k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 4 | Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas. | bactopia/ | 522 | — | ~1.3k | Automated safety check: Pass | MIT | 2 mo ago |
| 5 | Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report. | bactopia/ | 522 | — | ~4.9k | Automated safety check: Pass | MIT | 2 mo ago |
| 6 | Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools. | davila7/ | 32k | 12 repos | ~3.6k | Automated safety check: Pass | MIT | today |
| 7 | Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate. | bactopia/ | 522 | — | ~2.5k | Automated safety check: Pass | MIT | 2 mo ago |
| 8 | Latch platform for bioinformatics workflows. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 11 repos | ~2.4k | Automated safety check: Pass | MIT | today |
| 9 | Review staleness of reference docs under .agents/docs/ using bactopia-docs --validate. | bactopia/ | 522 | — | ~3.4k | Automated safety check: Pass | MIT | 2 mo ago |
| 10 | 10.Pacsomatic Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. | BioTender-max/ | 197 | — | ~1.3k | Automated safety check: Pass | MIT | 3 mo ago |
| 11 | Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. | K-Dense-AI/ | 48k | 1 repo | ~2.5k | Automated safety check: Notes | MIT | 2 days ago |
| 12 | 12.Pacsomatic Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. | K-Dense-AI/ | 48k | 1 repo | ~1.6k | Automated safety check: Pass | MIT | 2 days ago |
| 13 | Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. | K-Dense-AI/ | 48k | 1 repo | ~3.1k | Automated safety check: Pass | MIT | 2 days ago |
| 14 | 14.Nextflow Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. | K-Dense-AI/ | 48k | 1 repo | ~3.7k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 15 | Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline. | ClawBio/ | 1.2k | 3 repos | ~413 | Automated safety check: Pass | MIT | yesterday |
| 16 | Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills. | ClawBio/ | 1.2k | 1 repo | ~8.9k | Automated safety check: Pass | MIT | yesterday |
| 17 | Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 18 | Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. | GPTomics/ | 1.2k | 1 repo | ~4.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 19 | Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and… | GPTomics/ | 1.2k | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 20 | Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry… | GPTomics/ | 1.2k | 1 repo | ~4.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 21 | Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO… | GPTomics/ | 1.2k | 1 repo | ~4.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 22 | Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills. | ClawBio/ | 1.2k | — | ~13k | Automated safety check: Pass | MIT | yesterday |
| 23 | Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 370 | 2 repos | ~4k | Automated safety check: Pass | Apache-2.0 | 8 days ago |
| 24 | 24.Lamindb This skill is applicable when using LaminDB. An agent skill from aipoch/medical-research-skills. | aipoch/ | 2k | — | ~4.8k | Automated safety check: Pass | MIT | 20 days ago |
| 25 | Workflows for RNA-seq, GWAS, and variant calling in genomic research | wentorai/ | 298 | 1 repo | ~1.9k | Automated safety check: Pass | MIT | 3 mo ago |
| 26 | CD-GPT 生成式生物基础大模型，对 DNA/RNA/蛋白质序列预训练，支持单分子与多分子联合分析的预测与生成. An agent skill from infometa/workbuddyskills. | infometa/ | 342 | — | ~5k | Automated safety check: Pass | No licence | today |
| 27 | scPROTEIN 基于图神经网络，对单细胞蛋白组数据去批次效应降噪、不确定性估计、生成 embedding 与细胞类型表征，含 stage1/stage2 两子应用。 | infometa/ | 342 | — | ~5k | Automated safety check: Pass | No licence | today |
Questions, answered from the data.
What is the best Nextflow skill?
Add Bactopia Tool from bactopia/bactopia ranks first of the 27 Nextflow skills listed here, with the highest score: its repository has 522 GitHub stars, its SKILL.md loads about 4.1k tokens and it passes the automated safety check with no findings. Next come Bump Versions and Dockstore Release.
Is there an official Nextflow skill?
None yet. All 27 Nextflow skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.