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    Purpose and objective of EOSC-Life WP2

    An increasing number of studies describe workflows involving methods and tools from different domains of the life sciences. A high-level view of such workflows and corresponding publications is shown in figure 1. To run this type of workflow requires the tools within each workflow to be interoperable. The purpose of EOSC-Life WP2 is therefore to make software tools from the 13 LS RIs interoperable in the EOSC-Life cloud environment. The objective is to implement a software stack that makes tool interoperability possible and showcases the implemented solutions in related science demonstrators.

    Figure 1. Examples of workflows from publications in which the workflow is composed of tools from domains covered by different LS RIs.

    Scope of EOSC-Life WP2

    WP2 is concerned with computational tools and workflows that process biomedical data. For our purpose, the following definitions apply:

    In WP2, workflows are specified in terms of tools and manage the flow of data between the tools. We note that tools are not limited to the implementation of an atomic task but can also implement a workflow.

    For an introduction to the value of workflow management systems, see https://www.nature.com/articles/d41586-019-02619-z 7

    WP2 focuses on the part of the software stack required to implement workflows, namely tool packaging, containerisation, workflow management systems and other relevant platforms such as code notebooks. It doesn’t cover dealing with the provision and integration of cloud infrastructures. Cloud deployment is done in cooperation with EOSC-Life WP7.
    To maximise the use of WP2 resources and promote interoperability, WP2 will focus on a limited number of components and build upon resources already available.
    To promote findability and reusability, WP2 will unify tool and workflow descriptions using structured data, and provide a workflow registry that leverages current resources.

    Current WP2 roadmap

    Reviews of online materials and publications related to the activities of the LS RIs as well as informal discussions with individual researchers within some of the RIs (including during the project kick-off meeting) identified a range of tools and workflow systems in common use. This was complemented by a survey of the EOSC-Life science demonstrators. Based on this, WP2 has developed an initial technical roadmap that highlights technologies and standards that can be readily supported within the project. The technologies and standards include the Linux operating system, the Conda package manager, Singularity (and/or Docker) for containerisation, CWL for describing data analysis workflows, Nextflow for running workflows on the command line and the Galaxy platform as web-based UI for building and running data analysis workflows. In addition, there is growing interest in the use of RStudio and Jupyter notebooks. To build on existing efforts and expertise, WP2 will aim at using these tools or ensuring compatibility with them.

    Tool packaging and distribution

    The Open Container Initiative (OCI) develops open industry standards for container formats and runtimes.

    Workflows specification and management systems

    Workflow management system agnostic description and interoperability

    The Common Workflow Language (CWL) is selected as the standard for describing tools and workflows that can be executed by multiple workflow engines such as Nextflow and Snakemake. ELIXIR has invested in the support of CWL. CWL is also used by the EU’s BioExcel2 Centre of Excellence for Biomolecular modelling, and by the IBISBA ESFRI for Industrial Biotechnology. CWL is participating in GA4GH Task Execution API 1 (a minimal common API for submitting a single job to a remote execution endpoint) and GA4GH Workflow Execution API (a minimal common API for submitting workflow requests to workflow execution systems in a standardized way).
    http://www.commonwl.org 1

    Workflow Management Systems (WMS)

    EOSC Life aims to provide an environment to support a wide range of Workflow Management Systems available to its RI developers and users.
    Some workflow systems have been identified as meriting dedicated attention.

    Executable (Notebook) Environments

    Resources for Tools & Workflows