10 papers · ranked by Valyu relevance
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Marcin Cieślik, Cameron Mura
Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Malwina Kotowicz, Magdalena Shumanska, Sven Fengler, Birgit Kurkowsky + 14 more
'Birgit Kurkowsky' 'Anja Meyer-Berhorn' 'Elisa Moretti' 'Josephine Blersch' 'Gisela Schmidt' 'Jakob Kreye' 'Scott van Hoof' 'Elisa Sánchez-Sendín' 'S. Momsen Reincke' 'Lars Krüger' 'Harald Prüß' 'Philip Denner' 'Eugenio Fava' 'Dominik Stappert' 'Bhanwar Lal Puniya'] Data management and sample tracking in complex…
Taylor Reiter, Phillip T. Brooks, Luiz Irber, Shannon E.K. Joslin + 4 more
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter…
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang + 1 more
Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution…
Jason P. Kurs, Manuele Simi, Fabien Campagne
Computational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed…
Hugo López-Fernández, Osvaldo Graña-Castro, Alba Nogueira-Rodríguez, Miguel Reboiro-Jato + 2 more
'Miguel Reboiro-Jato' 'Daniel Glez-Peña' 'Robert Winkler'] Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii)…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
With pull-based workflow tools such as Snakemake or Luigi, it is easy to reproduce a particular output file on-demand because the scheduling mechanism is optimized for the use case of asking for a specific file and calculating all the tasks required to be executed based on that. With push-based workflow tools, however…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed…