Tutorials missing workflows

[shiltemann]

This is a list of tutorials that are missing a workflow, if anybody would like to run this tutorial and extract the workflow from their history afterwards and upload it here, this would be a great help for us!

• [ ] Topic: computational-chemistry Tutorial: setting-up-molecular-systems Link
• [ ] Topic: ecology Tutorial: species-distribution-modeling Link
• [x] Topic: epigenetics Tutorial: tal1-binding-site-identification Link
• [ ] Topic: genome-annotation Tutorial: genome-annotation Link
• [x] Topic: genome-annotation Tutorial: tnseq Link
• [x] Topic: introduction Tutorial: galaxy-intro-101 Link
• [ ] Topic: introduction Tutorial: galaxy-intro-ngs-data-managment Link
• [x] Topic: introduction Tutorial: galaxy-intro-peaks2genes Link
• [x] Topic: introduction Tutorial: igv-introduction Link
• [ ] Topic: introduction Tutorial: r-basics Link
• [x] Topic: proteomics Tutorial: labelfree-vs-labelled Link
• [x] Topic: transcriptomics Tutorial: rb-rnaseq Link
• [ ] Topic: transcriptomics Tutorial: rna-seq-counts-to-viz-in-r Link
• [x] Topic: transcriptomics Tutorial: scrna-plates-batches-barcodes Link
• [x] Topic: transcriptomics Tutorial: scrna-umis Link
• [x] Topic: variant-analysis Tutorial: non-dip Link
• [x] Topic: variant-analysis Tutorial: somatic-variants Link

And if you run into any other issues or questions when doing the tutorial, please add a fix or file an issue for it :)

[chrisbarnettster]

Trying out the Statistics and machine learning tutorial.

[hexylena]

Updated with fresh data, ca 75% of tutorials have workflows so that's great! :)

[hexylena]

@Delphine-L would you have a history where you could extract the tn-seq workflow? I have a user who wants to run that tutorial and want to make sure I've collected all the needed tools for it.

[malloryfreeberg]

Hi @hexylena @shiltemann !

I have created a workflow for the tutorial "tal1-binding-site-identification", and I have identified some updates to the existing tutorial that I am happy to put in a PR. I noticed that at the top of the tutorial it says "Under Development! This tutorial is not in its final state. The content may change a lot in the next months. Because of this status, it is also not listed in the topic pages.". So, I have two questions:

1. Does the TAL1 tutorial still need a workflow?
2. Would it be useful for me to make a PR with updates to the tutorial itself, or is someone else working on it?

Thanks! #Hacktoberfest

[hexylena]

Hi @malloryfreeberg I'm not sure anyone is currently working on it. It looks like it hasn't seen any updates in some time. If you have some updates to the tutorial itself to bring it up to quality, then that's fantastic! We can maybe set enable: true finally :) It looks like it still needs a WF so that would be great!

[malloryfreeberg]

Thanks @hexylena ! I have made the PR updating the TAL1 tutorial (https://github.com/galaxyproject/training-material/pull/2047) including adding a workflow and updating enabled: true.

I am happy to keep going through the tutorials listed in this ticket and generate workflows. The interface has changed quite a bit since I last used Galaxy - it looks great!

[malloryfreeberg]

I was going to generate a workflow for scrna-umis but realised there was no way to include a pasted text as input in the workflow-test.yml. I opened a ticket on the main Galaxy repo (https://github.com/galaxyproject/galaxy/issues/10415) and am happy to finish the workflow for this tutorial as a test case when this issue is addressed.

[malloryfreeberg]

Is it actually possible to make workflows for the R-based tutorials?

• Tutorial r-basics
• Tutorial: rna-seq-counts-to-viz-in-r

[hexylena]

Nope! Not currently. Maybe someday thanks to new ITs which are workflow compatible, we'll get that, but, not yet.

[nagaba-phionah]

@shiltemann i have done the tutorial workflow of Topic: introduction Tutorial: galaxy-intro-101 . please have a look at this https://usegalaxy.org/u/nagaba-phionah/h/galaxy-101 . maybe tell me whether its okay to do all of them. thanks uplicate of ### missing tutorial worflow of introduction Tutorial: galaxy-intro-101 #1459 solved

[bebatut]

@nagaba-phionah I am not sure to understand what you mean there

[shiltemann]

@nagaba-phionah The Galaxy 101 tutorial was already done (see checkmark in the list above).

You can also tell from the tutorial itself (this list might be out of date):

The workflows item under "supporting material" will link to the workflow file in the GTN:

You can still do this for one of the other tutorials still missing a workflow (but please check on the tutorial page if the workflow is really still missing). The idea is that once you have performed the entire tutorial, you extract a workflow from your history (instructions), and add the resulting workflow file to this repo.

[Alaa-Elghamry]

@bebatut Hi! I think I can help with this also, this list needs updating, some of the unchecked tutorials already have workflows