Bacterial Genome Assembly with Unicycler Training

[Delphine-L]

Hello, I am working on a Small genome Genome assembly training. This pull request is just here for information purpose, the material is still a work in progress. I would be grateful for any feedback on the material.

[bgruening]

@Delphine-L this is a very nice start! Thanks a lot for working on it!

[nekrut]

@Delphine-L give it a read!

[bgruening]

@Delphine-L is this ready to go or still WIP?

[Delphine-L]

@bgruening Im running the docker image to verify the tour one last time and it will be ready

[Delphine-L]

@bgruening It's ready to go !

[bgruening]

Give me a few minutes to check again - but I'm so motivated to get this in I will hurry up!

Thanks a lot!

[bgruening]

@Delphine-L a few comments included, but really just small things. Very well done!

[Delphine-L]

Thank you @bgruening ! I made the corrections.

[Delphine-L]

Thank you for your comments @bebatut ! I added key points and hands-on sections, however I am not sure if I should take the images out the sections for better readability or not, what do you think?

[shiltemann]

@Delphine-L I would say that if we list all the parameter settings clearly in text form (like the example code), that we maybe do not even need the screenshots at all (and this is also better for accessibility, and easier to update in the future). what do you think? (and otherwise I would say leave them inside the boxes because they are part of the hands-on segment)

[Delphine-L]

@shiltemann I removed the unused boxes and I replace the info box in the tutorial by a comment box. I changed the color of the comment box then. I also removed the pictures that were showing the tool parameters , replacing it by the description, but I let those that was showing less straight forward manipulations, I think it's more readable that way. What do you think?

[shiltemann]

@Delphine-L sounds good to me, thanks! we can think about the color scheme of the other box types too in some other PR then, if you feel more distinct colors are useful (I agree). Sorry to have been nitpicky, this really is an awesome tutorial, thanks a lot for making it!

[Delphine-L]

Thanks @bebatut ! I removed the hr tags and lines around images, it's more consistant that way. Do you think it's ready to be merged?

[nekrut]

@bebatut or @shiltemann : pls, merge as these errors don't make any sense

[nekrut]

@bebatut @Delphine-L @shiltemann errors are these:

- ./_site/topics/assembly/index.html
  *  External link https://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/slides.html failed: 404 No error
  *  External link https://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html failed: 404 No error
- ./_site/topics/assembly/tutorials/unicycler-assembly/tutorial.html
  *  External link https://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/slides failed: 404 No error
  *  External link https://github.com/galaxyproject/training-material/tree/master/topics/assembly/tutorials/unicycler-assembly/tutorial.md failed: 404 No error
htmlproofer 3.7.4 | Error:  HTML-Proofer found 4 failures!
make: *** [check] Error 1

Ok to merge?

[bebatut]

I was afraid to do it 😄

[bebatut]

https://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html 🎉

[shiltemann]

\o/ :tada: thanks a lot @Delphine-L @nekrut !