Adding tutorial on how to clean and manage AB1 files from Sanger sequencing #2718
Annotations
10 errors and 1 warning
Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga#L1
[rdjsonl] reported by reviewdog 🐶
This workflow is missing a license. Please select a valid OSI license. You can correct this in the Galaxy workflow editor.
Raw Output:
{"message":"This workflow is missing a license. Please select a valid OSI license. You can correct this in the Galaxy workflow editor.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:026","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn026"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga#L1
[rdjsonl] reported by reviewdog 🐶
This workflow is missing a Creator. Please edit this workflow in Galaxy to add the correct creator entities
Raw Output:
{"message":"This workflow is missing a Creator. Please edit this workflow in Galaxy to add the correct creator entities","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:024","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn024"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga#L1
[rdjsonl] reported by reviewdog 🐶
This workflow is missing a test, which is now mandatory. Please see [the FAQ on how to add tests to your workflows](https://training.galaxyproject.org/training-material/faqs/gtn/gtn_workflow_testing.html).
Raw Output:
{"message":"This workflow is missing a test, which is now mandatory. Please see [the FAQ on how to add tests to your workflows](https://training.galaxyproject.org/training-material/faqs/gtn/gtn_workflow_testing.html).","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:027","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn027"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga#L1
[rdjsonl] reported by reviewdog 🐶
This workflow is missing a license. Please select a valid OSI license. You can correct this in the Galaxy workflow editor.
Raw Output:
{"message":"This workflow is missing a license. Please select a valid OSI license. You can correct this in the Galaxy workflow editor.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:026","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn026"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga#L1
[rdjsonl] reported by reviewdog 🐶
This workflow is missing a Creator. Please edit this workflow in Galaxy to add the correct creator entities
Raw Output:
{"message":"This workflow is missing a Creator. Please edit this workflow in Galaxy to add the correct creator entities","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/main_workflow.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:024","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn024"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L530
[rdjsonl] reported by reviewdog 🐶
Please do not use 'here' as your link title, it is [bad for accessibility](https://usability.yale.edu/web-accessibility/articles/links#link-text). Instead try restructuring your sentence to have useful descriptive text in the link.
Raw Output:
{"message":"Please do not use 'here' as your link title, it is [bad for accessibility](https://usability.yale.edu/web-accessibility/articles/links#link-text). Instead try restructuring your sentence to have useful descriptive text in the link.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":530,"column":78},"end":{"line":530,"column":84}}},"severity":"ERROR","code":{"value":"GTN:005","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn005"},"suggestions":[{"text":"[Something better here]","range":{"start":{"line":530,"column":78},"end":{"line":530,"column":84}}}]}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L377
[rdjsonl] reported by reviewdog 🐶
This snippet (`tools_select_multiple_datasets.md`) does not seem to exist
Raw Output:
{"message":"This snippet (`tools_select_multiple_datasets.md`) does not seem to exist","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":377,"column":6},"end":{"line":377,"column":49}}},"severity":"ERROR","code":{"value":"GTN:008","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn008"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L173
[rdjsonl] reported by reviewdog 🐶
We have developed a new syntax for box titles, please consider using this instead.
Raw Output:
{"message":"We have developed a new syntax for box titles, please consider using this instead.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":173,"column":5},"end":{"line":173,"column":37}}},"severity":"ERROR","code":{"value":"GTN:010","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn010"},"suggestions":[{"text":"<question-title></question-title>","range":{"start":{"line":173,"column":5},"end":{"line":173,"column":37}}}]}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L176
[rdjsonl] reported by reviewdog 🐶
We have developed a new syntax for box titles, please consider using this instead.
Raw Output:
{"message":"We have developed a new syntax for box titles, please consider using this instead.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":176,"column":7},"end":{"line":176,"column":39}}},"severity":"ERROR","code":{"value":"GTN:010","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn010"},"suggestions":[{"text":"<solution-title></solution-title>","range":{"start":{"line":176,"column":7},"end":{"line":176,"column":39}}}]}
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Check Tutorial Formatting
reviewdog: Too many results (annotations) in diff.
You may miss some annotations due to GitHub limitation for annotation created by logging command.
Please check GitHub Actions log console to see all results.
Limitation:
- 10 warning annotations and 10 error annotations per step
- 50 annotations per job (sum of annotations from all the steps)
- 50 annotations per run (separate from the job annotations, these annotations aren't created by users)
Source: https://github.community/t5/GitHub-Actions/Maximum-number-of-annotations-that-can-be-created-using-GitHub/m-p/39085
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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-python@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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