Update bowtie2 to use PE collection in Mapping tutorial

[tflowers15]

Based on the GTN issue "Update tutorials to use collections instead of separate paired datasets #6377".

This update to the Mapping tutorial updates the version of bowtie2 used to 2.5.4+galaxy0 and replaces the separate paired end dataset inputs with a paired end collection (required PE input for this version of bowtie2). Also added the tool tip for creating paired end collections to the "Hands-on: Data upload".

[bernt-matthias]

Should there also be changes to the accompanying workflow(s)?

[shiltemann]

@bernt-matthias good point, are you up for changing the corresponding workflows as well @tflowers15? I can also help with that if you want, just say the word 👍

[tflowers15]

Updating the workflows completely slipped my mind.

Thank you for the offer, @shiltemann , but I should be able to update the workflows. The one part that I might need some help will be with updating the workflow tests, as I do not have a very good understanding of tests. But I'll see how I go as it is only the early parts of the workflows that need updating.

I'll work on updating the workflows and added them to these PRs before continuing with the other tutorials. Shall I convert the bowtie2 tutorial PRs back to draft until I have updated the workflows?

[shiltemann]

@tflowers15 Here is some information about adding workflow tests: https://galaxyproject.github.io/training-material/faqs/gtn/gtn_workflow_testing.html

Basically, if you run the workflow once on e.g. Galaxy Aus, you can automatically extract tests using PWDK: https://pwdk.apps.galaxyproject.eu/

So just see how you go and ping me if you would like a hand with that :)

as for draft mode, feel free to keep them as they are, Ill keep an eye on updates and you can always just leave a comment when it is ready from your side. And thanks again!

[tflowers15]

Thank you, @shiltemann . The part of workflow tests that I struggle with is understanding the syntax and what to put in the output checks. I think I should be able to just copy the output checks from the existing workflow test file into the newly created draft workflow test file as the output files being checked are not changing. I will update the input "class" as workflows will now use a collection.

[bernt-matthias]

Let us know if you have specific questions. FYI: Also the IWC has quite a lot of inpiration for workflow tests, e.g. paired collection input https://github.com/galaxyproject/iwc/blob/main/workflows/amplicon/dada2/dada2_paired-tests.yml