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docs/computing/running/toil-cwl-runner.md

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@@ -10,19 +10,32 @@ This page describes how run CWL worklflows on Puhti using `toil-cwl-runner`, inc
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## Strengths of the Common Workflow Language standards
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- Open standard (free to read, free to contribute to) governed by a [not-for-profit charity which is legally obligated to work in the public interest]([https://sfconservancy.org/](https://sfconservancy.org/news/2018/apr/11/cwl-new-member-project/)).
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- [Multiple implementations](https://www.commonwl.org/implementations/) of the CWL standards
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- Used in many [different fields of research](https://www.commonwl.org/gallery/)
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- YAML based syntax with [special support in many IDEs](https://www.commonwl.org/tools/#editors)
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- Support, but does not require, software containers. Can also work with conda packages, `module load` environments, and locally available software.
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- CWL's model works hard to keep site-specific deatuls out of the workflow definition. Enabling portability between laptops, clusters, and cloud systems.
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## Strengths of `toil-cwl-runner`
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- Supports sending jobs to Slurm, translating CWL resource requirements to Slurm resources specifications.
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- Can also run on other batch systems: Grid Engine, Torque, LSF, HTCondor.
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- Launches and monitors Slurm jobs for you. Also constructs the apptainer commands.
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## Disadvantages for using CWL
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## Disadvantages for using `toil-cwl-runner`
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- Just a workflow runner. Won't manage your data, or keep track of previous workflow runs.
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## Installing `toil-cwl-runner`
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(and nodejs)
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## Defining CWL workflows
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(link to existing docs)
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Learning resources
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- [Novice CWL tutorial](https://carpentries-incubator.github.io/cwl-novice-tutorial/), includes detailed setup instructions for local editing and running on Microsoft Windows, macOS, and Linux
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- <https://www.commonwl.org/user_guide/>
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## Running CWL workflows with `toil-cwl-runner`
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