RO-crate content appear in the nf-core lint warning if there is a TODO #3493
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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only one last comment, otherwise LGTM :)
I see the tests are failing, so we should fix this before merging. The reason is that when we create a fresh pipeline from the template, the ro-create file is not included. I think the best way would be to run nf-core pipelines ro-crate after creating the pipeline, on our CI
| else: | ||
| # Check if the 'description' key is present | ||
| if "description" not in graph[0]: | ||
| ignored.append( |
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it's not true that the test is ignored if there isn't a description no? If I am following correctly you assign an empty string and the test will run and fail if the README has a description
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Thanks for mentioning that! I changed it to simply coping the content from the readme file to the ro-crate-metadata if there's no 'description' key. Another general question would be how to handle these failed tests when it failed the ignored tests? For example this one:
Run no-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned
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In the tests we are creating an empty ro-crate file (here). I think if we run nf-core pipelines ro-crate instead, the tests will pass
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moved this from To do
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in Hackathon March 2025
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
| else: | ||
| # Check if the 'description' key is present | ||
| if "description" not in graph[0]: | ||
| ignored.append( |
There was a problem hiding this comment.
In the tests we are creating an empty ro-crate file (here). I think if we run nf-core pipelines ro-crate instead, the tests will pass
Changes:
RO-crate-metadata.jsonis ignored in lintingnf_core/pipelines/lint/rocrate_readme_sync.pyfor synchronizing the content of ROcrate metadata and the repo README.The warning message mentioned here disappears when you create a new pipeline without deleting the TODO commands. But I still wonder where I should add the
--fixflag so that the use can decide whether they want to synchronize the metadata with the readme file.PR checklist
CHANGELOG.mdis updateddocsis updated