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Writing Paper (JOSS) - #188
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Co-authored-by: aleidel <162713718+aleidel@users.noreply.github.com>
Co-authored-by: aleidel <162713718+aleidel@users.noreply.github.com>
Co-authored-by: aleidel <162713718+aleidel@users.noreply.github.com>
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October 21, 2026 13:22
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@XaverStiensmeier @patrick-koenig @gannebamm @hvwaldow As you are listed as authors for this paper, please take your chance to review. |
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Is it possible to get a compiled version of it? Don't have a setup to build this at hand at the moment |
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Nice short paper introducing the concept and implementation to the world. Comprehensive and snappy to read. Great work!
| Bringing such individual scripts into established workflow platforms can present a substantial hurdle. With Nextflow, researchers need to learn the Groovy-based workflow DSL. In Galaxy, tools may need to undergo a curation and integration process before they become available on a public usegalaxy.* server. Moreover, workflows authored for Galaxy are often coupled to the capabilities and configuration of a particular Galaxy instance, and portability across infrastructures may require additional adaptation. | ||
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| CWL was introduced as a vendor-neutral, platform agnostic standard to address fragmentation and portability. There were efforts to make Galaxy and Nextflow compliant to this standard [@DiTommaso.2018]. However, the cwl2nxf converter for Nextflow was archived in 2025, and CWL support in Galaxy has been an open draft since 2021 [@Soranzo.2021]. Snakemake has `--export-cwl` which however just wraps a call to the Snakemake program in a CWL description using the Snakemake Docker container. | ||
| The adoption of CWL remains lower than that of Snakemake, Nextflow and Galaxy. Its verbose, YAML-based syntax requires familiarity with structured data formats and workflow abstractions that many domain researchers do not possess. The CWL ecosystem further compounds this problem. While a number of number of great runner implementations exist (e.g. cwltool, Toil [@Vivian.2017], REANA, Arvados)[@{CommonWorkflowLanguage.b}], they require the Windows Subsystem for Linux (WSL) on Windows. Moreover, the space of authoring tools is sparse [@{CommonWorkflowLanguage.}]. Rabix offered a graphical editor (Rabix Composer)[@Kaushik.2016] but further development was made closed-source and moved into the Seven Bridges Platform [@RabixComposercontributors.2021]. The open-sourced version has been unmaintained for over 5 years and is significantly outdated. Many other generators like `scriptcwl` [@Van_der_zwaan.2019] (last commit 2020) are outdated as well or restricted to Python, Python argparse programs or webforms like `Janis` [@PMCCBioinformaticsCore.2023] (last commit 2023), `argparse2tool`[@Rasche.2024] (last commit 2024) or `ToolJig` [@Piccolo.2021]. The `zatsu-cwl-generator` [@Tanjo.2022] (last commit 2022) is the closest to our approach, but it parses a command without running it, so it cannot observe files the command creates. |
| SciWIn-Client provides an intuitive command-line interface that automates CWL generation and management. It translates typical research computing tasks into structured, version-controlled workflow definitions, effectively allowing scientists to "write CWL by doing science." | ||
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| # State of the field | ||
| Tools such as Nextflow [@DiTommaso.2017], Snakemake [@Molder.2021] and Galaxy [@Giardine.2005;@TheGalaxyCommunity.2024] have achieved significant adoption within the scientific community. They offer powerful execution environments and rich graphical or scripting environments. Significant effort was put in providing a broad set of workflows especially for the OMICS-community (e.g. nf-core [@Ewels.2020]), but they are lacking in the agro-community where individual scripting plays a key part. |
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Is there any evidence for the lack of use in agro community, eg a survey?
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The left side with local / reana... Should be an OR.
Maybe visually separate those a bit and put in an '/' between them?
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Commit and/or merge changes to the paper to this branch
Invite people for proof read if their products products: Middleware, Search, ARCs, ... are mentioned in a way we need an approval.
When draft is ready spread into TA4 at least BEFORE publishing!
This PR is used for communication and CI Builds, it may never will be merged to master!