Add "Adding workflows" section, improve main readme #41
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mvdbeek
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| Workflows are categorized in the [workflows](workflows/) directory, and listed in [Dockstore](https://dockstore.org/organizations/iwc) and [WorkflowHub](https://workflowhub.eu/search?utf8=%E2%9C%93&q=IWC#workflows). | ||
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| All workflows are reviewed and tested before and after publication, follow [best practices](https://planemo.readthedocs.io/en/latest/best_practices_workflows.html) and contain explicit versions and rich metadata, including: |
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Why "after publication"?
Maybe repace "and contain" by ", contain"
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We're going to test those workflows regularly, but let me make that more specific
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| To import IWC workflows into your Galaxy instance use the TRS workflow search in the Galaxy interface. | ||
| Click on "Workflows", "Import" and click on the "search form" link. | ||
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The gif is cool. Would be even better if the workflows that are shown as result of the search would have a description.
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Yeah, that's a problem with gxformat2, I think. I'll update the gif once that's done.
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Interestingly, the organization column also doesn't get populated, but this info is available.
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Yeah, the vue component needs a little kick :)
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Also seek4science/seek#637 would give us a chance to explore organizations. If you want to thumb up that issue maybe it'll move up the priorities ? 😄
README.md
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| ## Becoming a IWC member | ||
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| Everyone is welcome and can help out with reviewing or creating workflows. Post a comment [here](https://github.com/galaxyproject/iwc/issues/4) with your expertise and we will add you to the IWC organization. |
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Sounds a bit as if reviewing and creating workflows is only possible as IWC member.
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Right, I'll rewrite that to say Everyone is welcome and can help out with reviewing workflows.
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Really nice! In line 12 of the workflows/ README, you could maybe link directly to https://planemo.readthedocs.io/en/latest/test_format.html instead of to the planemo github repo? |
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In the ro-crate section, it's a bit unclear whom the script is for, i.e. who's supposed to generate the data? |
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Yeah, let me move that into the deployment process, we can autogenerate this. The fewer things people need to submit the better IMO. We could probably even autogenerate the .dockstore.yml file, but that is a shortcut for planemo to find directories that should become a repository, so we do need this right now. |
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| To import IWC workflows into your Galaxy instance use the TRS workflow search in the Galaxy interface. | ||
| Click on "Workflows", "Import" and click on the "search form" link. | ||
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Can you add a note under that animation saying: when searching against workflowhub.eu, please use organization:"IWC Workflows" as the search term?
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This needs to be fixed on the workflowhub side. iwc is the right organization name.
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Do you have a workflowhub account ? I do, but I can't log in, hanging in a loop. If you do, maybe you could submit the form https://workflowhub.eu/home/feedback ?
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Finally managed it in a private session.
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Well, yes and no:
- I don't quite understand what dockstore is doing either: when you look at the WFs returned by the organization:iwc query, they all list "iwc-workflows" as the organization (though undoubtedly we're iwc on the dockstore website). Not sure whether the query only works accidentally (organization:workflows seems to be working just as well).
- Until this is unified upstream, we might still want to provide working instructions here (and simplify it later)?
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Alright, with Denis' response I looked a bit closer, and searching for iwc-workflows should also return our workflows. So galaxyproject/galaxy#12196 fixes that in Galaxy. So then I guess it's somewhat consistent. I updated the gif too.
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For information, when I follow exactly the gif instructions (Galaxy search form), the search works only with "iuc" and fails if I add "-workflows" or anything after "iuc"
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Thanks, yeah, that will be fixed in galaxyproject/galaxy#12196
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@drosofff quoting the organization name is what's working right now, i.e. organization:"iwc-workflows" for dockstore and organization:"IWC Workflows" for workflowhub.
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I've deployed the update to usegalaxy.org, so organization:iwc-workflows works there.
Co-authored-by: Wolfgang Maier <maierw@posteo.de>
And mention that they don't need to be generated right now. Looking at this more closely I think we should move the RO-Crate generation to either planemo-ci-action, or planemo itself.
Hope that'll be fixed with galaxyproject/dockstore-galaxy-interface#19 |
Co-authored-by: Wolfgang Maier <maierw@posteo.de>
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I'm gonna go with @bernt-matthias' approval :). We can (and should) revisit this whenever we have updates. Thanks for the reviews @bernt-matthias @wm75 @drosofff! |
I've written this up while creating #40, so this should include all steps