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common-workflow-language
The CWL v1.0 - v1.2 user guide
These are lessons 19 & 20 A smaller tool can have a small Docker container and would be more easily used & tested For "Custom Types", we could use https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/tools/biom-convert.cwl...
https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/writable-dir-docker.cwl can be adapted as an example
- [ ] how to minimize a test case - [ ] how to add it to the conformance tests suite; best practices around naming and labels, etc.
http://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement and `linkMerge` from http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput
Basic approach https://gitter.im/common-workflow-language/common-workflow-language?at=5a7dd419e217167e2c638153 But should use a better example than a File's path
This lesson needs to make very clear that only some CWL engines support this extension, but that it is planned for CWL v1.1 Known implementors: - cwlref-runner - arvados Need...
In order of visibility to users: 1. Workflow level inputs (without defaults) these are mandatory 2. Workflow level inputs (**with** defaults) these are optional 3. Tool inputs set at the...
the example should also include a `SoftwareRequirement` hint, using RRID.
Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx) to permit the latest version. Release notes Sourced from sphinx's releases. Sphinx 8.0.0 Changelog: https://www.sphinx-doc.org/en/master/changes.html Dependencies #12633: Drop Python 3.9 support. Incompatible changes Remove deprecated...
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot] avatar"){kind=avatar}
http://www.commonwl.org/user_guide/rec-practices/ is a 404 Linked to from https://view.commonwl.org/about and https://github.com/common-workflow-library/bio-cwl-tools/blob/release/CONTRIBUTING.md and other places