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The nf-core framework for community-curated bioinformatics pipelines
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The nf-core framework for community-curated bioinformatics pipelines (2020)The nf-core framework for community-curat…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…WorkflowHub: a registry for computational workflows (2025)WorkflowHub: a registry for c…Empowering bioinformatics communities with Nextflow and nf-core (2025)Empowering bioinformatics com…An AI Agent for Fully Automated Multi‐Omic Analyses (2024)An AI Agent for Fully Automat…Ten quick tips for building FAIR workflows (2023)Ten quick tips for building F…Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems (2023)Developing and reusing bioinf…Using prototyping to choose a bioinformatics workflow management system (2021)Using prototyping to choose a…The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols (2021)The Dockstore: enhancing a co…Streamlining data-intensive biology with workflow systems (2021)Streamlining data-intensive b…Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Reproducible, scalable, and s…Design considerations for workflow management systems use in production genomics research and the clinic (2021)Design considerations for wor…Bioimage analysis workflows: community resources to navigate through a complex ecosystem (2021)Bioimage analysis workflows: …A Community Roadmap for Scientific Workflows Research and Development (2021)A Community Roadmap for Scien…Practical guide for managing large-scale human genome data in research (2020)Practical guide for managing …DolphinNext: a distributed data processing platform for high throughput genomics (2020)DolphinNext: a distributed da…CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content (2020)CoproID predicts the source o…Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites (2020)Can reproducibility be improv…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Snakemake—a scalable bioinformatics workflow engine (2012)Reproducibility: A tragedy of errors (2016)Sustainable data analysis with Snakemake (2021)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)A manifesto for reproducible science (2017)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Galaxy: A platform for interactive large-scale genome analysis (2005)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Singularity: Scientific containers for mobility of compute (2017)BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud (2018)A global reference for human genetic variation (2015)Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all (2023)Sustainable data analysis with Snakemake (2021)HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data (2024)Principles for data analysis workflows (2021)Spatial machine learning: new opportunities for regional science (2021)Leveraging large language models for data analysis automation (2025)Streamline automated biomedical discoveries with agentic bioinformatics (2025)BioMaster: Multi-agent system for automated bioinformatics analysis workflow (2026)
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References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited

Cited by

  • 2021Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers228 cited
  • 2020DolphinNext: a distributed data processing platform for high throughput genomics103 cited
  • 2024An AI Agent for Fully Automated Multi‐Omic Analyses89 cited
  • 2025Empowering bioinformatics communities with Nextflow and nf-core64 cited
  • 2020Practical guide for managing large-scale human genome data in research62 cited
  • 2021Streamlining data-intensive biology with workflow systems60 cited
  • 2020CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content57 cited
  • 2021A Community Roadmap for Scientific Workflows Research and Development49 cited
  • 2025WorkflowHub: a registry for computational workflows46 cited
  • 2021Design considerations for workflow management systems use in production genomics research and the clinic

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43 cited
  • 2023Ten quick tips for building FAIR workflows42 cited
  • 2023Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems41 cited
  • 2020Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites34 cited
  • 2021The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols34 cited
  • 2021Using prototyping to choose a bioinformatics workflow management system28 cited
  • 2021Bioimage analysis workflows: community resources to navigate through a complex ecosystem22 cited