SciWIn Client - Scientific Workflow Infrastructure<!-- omit from toc -->

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📖 Table of Contents<!-- omit from toc -->

• 🚀 About
• 🏗️ How to Build and Test
• 🎯 Installation
• 📚 How to Use
  • Project initialization
  • Creation of CWL CommandLineTools
  • Creation of CWL Workflows
  • Execution of CWL Files
• 🪂 Contributors
• ⚖️ License

🚀 About

Computational workflows, which describe complex, multi-step procedures for automated execution, are essential for ensuring reproducibility, scalability, and efficiency in scientific research. The FAIRagro Scientific Workflow Infrastructure (SciWIn) supports scientists to create, execute, share, and publish these workflows, fostering collaboration and transparency.

Reproducibility in computational research is vital for efficient collaboration, verifying results and ensuring transparency. Yet it remains challenging due to complex workflows, inconsistent data management and the reliance on specific software environments. SciWIn Client is a command-line tool designed to easily create, record, annotate and execute computational workflows. SciWIn Client enables researchers to interactively use intuitive commands to keep track of tasks such as as data-extraction, -cleaning, -transformation, -analysis, -visualization and computational simulation. Automated and standardised workflows minimise sources of error and support transparent and reproducible Open Science.

🏗️ How to Build and Test

This project is being developed using Rust and Cargo. To run the source code use cargo run, to build use cargo build.

To run the tests use cargo test or cargo test -- --nocapture to output logs.

```bash

Clone the repository

git clone https://github.com/fairagro/m4.4sciwinclient cd m4.4sciwinclient

Build the project

cargo build

Run the project

cargo run ```

To run tests (unit and integration) bash cargo test --workspace # Run all tests cargo test -- --nocapture # Show log output during tests

🎯 Installation

Detailed installation instructions can be found at the latest release:

The easiest way is to use the shell or powershell scripts with the provided commands. To install latests binaries you can use the following scripts:

Linux/MacOS:

bash curl --proto '=https' --tlsv1.2 -LsSf https://fairagro.github.io/m4.4_sciwin_client/get_s4n.sh | sh

Windows:

powershell powershell -ExecutionPolicy Bypass -c "irm https://fairagro.github.io/m4.4_sciwin_client/get_s4n.ps1 | iex"

📚 How to Use

Take a look at the User documentation. An overview on how to use SciWIn Client is available below.

Project initialization

Most commands need the context of a Git repo to work. Project initialization can be done using the s4n init command. bash s4n init -p <FOLDER/PROJECT NAME> Besides the minimal project structure, the creation of an "Annotated Research Context" or ARC is also possible. bash s4n init -a -p <FOLDER/PROJECT NAME>

Creation of CWL CommandLineTools

To create CWL CommandLineTools which can be combined to workflows later a prefix command can be used. s4n tool create which has s4n run as a synonym will execute any given command and creates a CWL CommandLineTool accordingly. bash s4n tool create <COMMAND> [ARGUMENTS] The command comes with a lot of different options on how to handle the CWL creation specifically. ``` Usage: s4n tool create [OPTIONS] [COMMAND]...

Arguments: [COMMAND]... Command line call e.g. python script.py [ARGUMENTS]

Options: -n, --name A name to be used for this tool -c, --container-image An image to pull from e.g. docker hub or path to a Dockerfile -t, --container-tag The tag for the container when using a Dockerfile -r, --raw Outputs the raw CWL contents to terminal --no-commit Do not commit at the end of tool creation --no-run Do not run given command --clean Deletes created outputs after usage ```

Creation of CWL Workflows

CWL Workflows can be created semi-automatically using s4n workflow commands. First of all a workflow needs to be created. bash s4n workflow create <NAME> After execution of this command a file called workflows/<NAME>/<NAME>.cwl will be created. Workflow Steps and Connections can be added using the s4n workflow connect command. Connections to In- or Outputs are added using either @inputs or @outputs as file identifier. bash s4n workflow connect <NAME> --from [FILE]/[SLOT] --to [FILE/SLOT] For example: s4n workflow connect demo --from @inputs/speakers --to calculation/speakers - The Step calculation will be added pointing to workflows/calculation/calculation.cwl, which will use the newly created input speakers as input for its speakers input.

Execution of CWL Files

SciWIn-Client comes with its custom CWL Runner (which does not support all cwltool can do, yet!) to run Workflows and CommandLineTools. The command s4n execute local can also be triggered using s4n ex l. bash s4n execute local <CWLFILE> [ARGUMENTS]

🪂 Contributors

Made with contrib.rocks.

|Measure 4.4||| |--|--|--| |Jens Krumsieck|:octocat: @jenskrumsieck|ORCID: 0000-0001-6242-5846| |Antonia Leidel|:octocat: @aleidel|ORCID: 0009-0007-1765-0527| |Patrick König|:octocat: @patrick-koenig|ORCID: 0000-0002-8948-6793| |Xaver Stiensmeier|:octocat: @XaverStiensmeier|ORCID: 0009-0005-3274-122X| |Harald von Waldow|:octocat: @hvwaldow|ORCID: 0000-0003-4800-2833|

⚖️ License

This work is dual-licensed under Apache 2.0 and MIT . You can choose between one of them if you use this work. SPDX-License-Identifier: Apache-2.0 OR MIT

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