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Simplifying the development of portable, scalable, and reproducible workflows
16 references·1 citing·31 second hop
Simplifying the development of portable, scalable, and reproducible workflows (2021)Simplifying the development of portable, …Ten simple rules for writing Dockerfiles for reproducible data science (2020)Ten simple rules for writing …CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language (2019)CWL-Airflow: a lightweight pi…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Binder 2.0 - Reproducible, interactive, sharable environments for science at scale (2018)Binder 2.0 - Reproducible, in…Toil enables reproducible, open source, big biomedical data analyses (2017)Toil enables reproducible, op…The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows (2017)The Dockstore: enabling modul…Singularity: Scientific containers for mobility of compute (2017)Singularity: Scientific conta…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…Tools and techniques for computational reproducibility (2016)Tools and techniques for comp…Common Workflow Language, draft 3 (2016)Common Workflow Language, dra…A review of bioinformatic pipeline frameworks (2016)A review of bioinformatic pip…An introduction to Docker for reproducible research (2015)An introduction to Docker for…Best Practices for Scientific Computing (2014)Best Practices for Scientific…Snakemake—a scalable bioinformatics workflow engine (2012)Snakemake—a scalable bioinfor…The Fourth Paradigm: Data-Intensive Scientific Discovery (2009)The Fourth Paradigm: Data-Int…How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools (2026)How to make big data accessib…Reproducible Research in Computational Science (2011)Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation (2016)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Automated assessment of psychiatric disorders using speech: A systematic review (2020)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Sustainable data analysis with Snakemake (2021)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Towards FAIR principles for research software (2019)Towards reproducible computational drug discovery (2020)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Reproducibility: A tragedy of errors (2016)The nf-core framework for community-curated bioinformatics pipelines (2020)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)WaveLab and Reproducible Research (1995)Statistical Analyses and Reproducible Research (2007)Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks (2019)Using Jupyter for Reproducible Scientific Workflows (2021)A large-scale study on research code quality and execution (2022)Good enough practices in scientific computing. (2017)Our path to better science in less time using open data science tools (2017)A Large-Scale Study About Quality and Reproducibility of Jupyter Notebooks (2019)Sustainable data analysis with Snakemake (2021)Methods included (2022)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Temporal Patterns of Happiness and Information in a Global Social Network: Hedonometrics and Twitter (2011)Toward Scalable Systems for Big Data Analytics: A Technology Tutorial (2014)GeoAI: spatially explicit artificial intelligence techniques for geographic knowledge discovery and beyond (2019)
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References

  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2012Snakemake—a scalable bioinformatics workflow engine2,775 cited
  • 2017Singularity: Scientific containers for mobility of compute2,734 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2009The Fourth Paradigm: Data-Intensive Scientific Discovery1,415 cited
  • 2017Toil enables reproducible, open source, big biomedical data analyses1,362 cited
  • 2015An introduction to Docker for reproducible research1,058 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2014Best Practices for Scientific Computing715 cited
  • 2018Binder 2.0 - Reproducible, interactive, sharable environments for science at scale302 cited
  • 2016A review of bioinformatic pipeline frameworks250 cited
  • 2016Common Workflow Language, draft 3204 cited
  • 2016Tools and techniques for computational reproducibility169 cited
  • 2020Ten simple rules for writing Dockerfiles for reproducible data science107 cited
  • 2017The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

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83 cited
  • 2019CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language65 cited
  • Cited by

    • 2026How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools10 cited