Adding tutorial on how to clean and manage AB1 files from Sanger sequencing #2723
Annotations
10 errors and 5 warnings
Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST-tests.yml#L1
[rdjsonl] reported by reviewdog ๐ถ
There are colons in this filename, that is forbidden.
Raw Output:
{"message":"There are colons in this filename, that is forbidden.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST-tests.yml","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:014","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn014"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga#L1
[rdjsonl] reported by reviewdog ๐ถ
There are colons in this filename, that is forbidden.
Raw Output:
{"message":"There are colons in this filename, that is forbidden.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:014","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn014"}}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga#L1
[rdjsonl] reported by reviewdog ๐ถ
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/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.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/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga#L1
[rdjsonl] reported by reviewdog ๐ถ
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/Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.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/Training-Sanger-sequences-CHD8.ga#L1
[rdjsonl] reported by reviewdog ๐ถ
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 ๐ถ
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 ๐ถ
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 ๐ถ
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 ๐ถ
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
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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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L173
[rdjsonl] reported by reviewdog ๐ถ
It is no longer necessary to prefix your question box titles with Question, this is done automatically.
Raw Output:
{"message":"It is no longer necessary to prefix your question box titles with Question, this is done automatically.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":173,"column":21},"end":{"line":173,"column":29}}},"severity":"WARNING","code":{"value":"GTN:022","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn022"},"suggestions":[{"text":"","range":{"start":{"line":173,"column":21},"end":{"line":173,"column":29}}}]}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L176
[rdjsonl] reported by reviewdog ๐ถ
It is no longer necessary to prefix your solution box titles with Solution, this is done automatically.
Raw Output:
{"message":"It is no longer necessary to prefix your solution box titles with Solution, this is done automatically.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":176,"column":23},"end":{"line":176,"column":31}}},"severity":"WARNING","code":{"value":"GTN:022","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn022"},"suggestions":[{"text":"","range":{"start":{"line":176,"column":23},"end":{"line":176,"column":31}}}]}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L510
[rdjsonl] reported by reviewdog ๐ถ
It is no longer necessary to prefix your question box titles with Question, this is done automatically.
Raw Output:
{"message":"It is no longer necessary to prefix your question box titles with Question, this is done automatically.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":510,"column":21},"end":{"line":510,"column":29}}},"severity":"WARNING","code":{"value":"GTN:022","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn022"},"suggestions":[{"text":"","range":{"start":{"line":510,"column":21},"end":{"line":510,"column":29}}}]}
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Check Tutorial Formatting:
topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md#L513
[rdjsonl] reported by reviewdog ๐ถ
It is no longer necessary to prefix your solution box titles with Solution, this is done automatically.
Raw Output:
{"message":"It is no longer necessary to prefix your solution box titles with Solution, this is done automatically.","location":{"path":"./topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.md","range":{"start":{"line":513,"column":23},"end":{"line":513,"column":31}}},"severity":"WARNING","code":{"value":"GTN:022","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn022"},"suggestions":[{"text":"","range":{"start":{"line":513,"column":23},"end":{"line":513,"column":31}}}]}
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