Add new tutorial for deciphering viral populations using SNV and baculovirus isolates (Variant analysis)

[wennj]

Dear GTN Team,

I am a new contributor and have created a tutorial for analysing virus populations using SNV (and using the example of large dsDNA viruses). The workflow is based on published results and follows a scientific approach. I have followed the GTN instructions as closely as possible (and as I understand them). Please excuse any mistakes in using Github. The tutorial has also been reviewed by a student.

Key changes:

• Added a new step-by-step tutorial (variant-analysis/baculovirus-isolate-variation) for analysing viral populations on the example of baculovirus isolates
• CONTRIBUTORS.yaml was changed.

Checked:

• Images can be re-hosted.

Help:

• One image in the introduction is linked to ICTV.global. Allowed?

TODO:

• Tool bcftools mpileup / bcftools call are using DPR (deprecated but functional). Needs to be changed to AD in the future.
• Awaiting feedback and suggestions for improvement.
• Refine the tutorial based on reviewer comments.

Best,
JTW

[bgruening]

Very cool! Welcome @wennj!

I have added a few batch of comments, if you agree with them you can accept them from inside the github interface.

[wennj]

Very nice work @wennj ! Those awk expressions are rather intimidating for beginners I guess, but also elegant compared to multi-step solutions with other tools. Can be interesting to teach them :-)

Thank you for your time, the valuable comments and suggestions @wm75 . It took a while to make all the necessary changes but I think that all the comments have been addressed. The tutorial has improved!

[wm75]

The remaining CI issues are:

{"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/variant-analysis/tutorials/baculovirus-isolate-variation/workflows/main_workflow.ga","range":{"start":{"line":1,"column":1},"end":{"line":1,"column":1}}},"severity":"ERROR","code":{"value":"GTN:027","url":"https://training.galaxyproject.org/training-material/gtn_rdoc/Gtn/Linter.html#method-c-"}}
{"message":"This looks like a DOI which could be better served by using the built-in Citations mechanism. You can use https://doi2bib.org/ to convert your DOI into a .bib formatted entry, and add to your tutorial.md","location":{"path":"./topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.md","range":{"start":{"line":202,"column":97},"end":{"line":202,"column":159}}},"severity":"WARNING","code":{"value":"GTN:004","url":"https://training.galaxyproject.org/training-material/gtn_rdoc/Gtn/Linter.html#method-c-check_dois"},"suggestions":[{"text":"{% cite ... %}","range":{"start":{"line":202,"column":97},"end":{"line":202,"column":159}}}]}
{"message":"Please do not include an # Introduction section, it is unnecessary here, just start directly into your text. The first paragraph that is seen by our infrastructure will automatically be shown in a few places as an abstract.","location":{"path":"./topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.md","range":{"start":{"line":1,"column":1},"end":{"line":2,"column":1}}},"severity":"ERROR","code":{"value":"GTN:046","url":"https://training.galaxyproject.org/training-material/gtn_rdoc/Gtn/Linter.html#method-c-useless_intro"},"suggestions":[{"text":"","range":{"start":{"line":1,"column":1},"end":{"line":2,"column":1}}}]}

Let me know if you have trouble with the workflow tests ...

... and please remember to pull my changes first before continuing to work on your local version.

[wennj]

@wm75 I think I pulled your changes this time. And I'm starting to understand how the automated tests work. I have added the workflow test files, as well. Let me know if any changes are required. Sorry for the trouble with the Gemfile.lock.

[wennj]

@wm75 Sorry also from my side for the late feedback. Very busy this week.
I am a bit confused now what to do with the WF tests. 1. I can leave them as they are for now, although they make few sense and add changes as suggested by you later. 2. I remove the WF tests entirely for now and add updated WF tests later. 3. I add your suggested changed to the WF tests which would require significant changes.

[wm75]

@wm75 Sorry also from my side for the late feedback. Very busy this week. I am a bit confused now what to do with the WF tests. 1. I can leave them as they are for now, although they make few sense and add changes as suggested by you later. 2. I remove the WF tests entirely for now and add updated WF tests later. 3. I add your suggested changed to the WF tests which would require significant changes.

Let me see if I can come up with something this week :-)

[wennj]

@wm75 Sorry also from my side for the late feedback. Very busy this week. I am a bit confused now what to do with the WF tests. 1. I can leave them as they are for now, although they make few sense and add changes as suggested by you later. 2. I remove the WF tests entirely for now and add updated WF tests later. 3. I add your suggested changed to the WF tests which would require significant changes.

Let me see if I can come up with something this week :-)

Do you already have an idea? I am motivated to continue working on the tutorial, even though it is merged.

[wm75]

I changed the tests now to confirm that expected content is present in the workflow outputs and removed the test-data files (which we would likely have had to update on any future change).

Lets get this live and see how it goes :-)