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Design considerations for workflow management systems use in production genomics research and the clinic
16 references·4 citing·29 second hop
Design considerations for workflow management systems use in production genomics research and the clinic (2021)Design considerations for workflow manage…The nf-core framework for community-curated bioinformatics pipelines (2020)The nf-core framework for com…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…Toil enables reproducible, open source, big biomedical data analyses (2017)Toil enables reproducible, op…The future of scientific workflows (2017)The future of scientific work…Practical Computational Reproducibility in the Life Sciences (2017)Practical Computational Repro…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…A characterization of workflow management systems for extreme-scale applications (2017)A characterization of workflo…A review of bioinformatic pipeline frameworks (2016)A review of bioinformatic pip…Big Data: Astronomical or Genomical? (2015)Big Data: Astronomical or Gen…Big data and its technical challenges (2014)Big data and its technical ch…Snakemake—a scalable bioinformatics workflow engine (2012)Snakemake—a scalable bioinfor…Beyond the Data Deluge (2009)Beyond the Data DelugeWorkflows and e-Science: An overview of workflow system features and capabilities (2008)Workflows and e-Science: An o…Workflow Patterns (2003)Workflow PatternsTen quick tips for building FAIR workflows (2023)Ten quick tips for building F…Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice (2023)Building Domain-Specific Mach…Accelerating bioinformatics implementation in public health (2023)Accelerating bioinformatics i…Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development (2021)Workflows Community Summit: A…Big data: The next frontier for innovation, competition, and productivity (2011)Big Data and cloud computing: innovation opportunities and challenges (2016)Debating big data: A literature review on realizing value from big data (2017)Machine Learning With Big Data: Challenges and Approaches (2017)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Sustainable data analysis with Snakemake (2021)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Geospatial Cyberinfrastructure: Past, present and future (2010)Reproducibility in Scientific Computing (2018)Reproducibility: A tragedy of errors (2016)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)An overview of workflow management: From process modeling to workflow automation infrastructure (1995)THE APPLICATION OF PETRI NETS TO WORKFLOW MANAGEMENT (1998)Business Process Management: A Survey (2003)YAWL: yet another workflow language (2004)Scientific workflow management and the Kepler system (2005)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)Situating Ecology as a Big-Data Science: Current Advances, Challenges, and Solutions (2018)A Roadmap for HEP Software and Computing R&D for the 2020s (2019)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Sustainable data analysis with Snakemake (2021)Methods included (2022)DolphinNext: a distributed data processing platform for high throughput genomics (2020)An AI Agent for Fully Automated Multi‐Omic Analyses (2024)
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References

  • 2020The nf-core framework for community-curated bioinformatics pipelines4,089 cited
  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2012Snakemake—a scalable bioinformatics workflow engine2,775 cited
  • 2003Workflow Patterns2,613 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2017Toil enables reproducible, open source, big biomedical data analyses1,362 cited
  • 2015Big Data: Astronomical or Genomical?1,340 cited
  • 2014Big data and its technical challenges1,049 cited
  • 2008Workflows and e-Science: An overview of workflow system features and capabilities832 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2009Beyond the Data Deluge535 cited
  • 2016A review of bioinformatic pipeline frameworks250 cited
  • 2017The future of scientific workflows182 cited
  • 2017Practical Computational Reproducibility in the Life Sciences158 cited

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2017
A characterization of workflow management systems for extreme-scale applications
149 cited

Cited by

  • 2023Ten quick tips for building FAIR workflows42 cited
  • 2023Accelerating bioinformatics implementation in public health26 cited
  • 2021Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development15 cited
  • 2023Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice10 cited