Workflow Documentation

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Hi everyone,

I made a workflow in galaxy for processing sequencing data for my doctoral thesis and am currently wondering what description is suited best for documentation of the workflow. E.g. would the information of workflow file in .ga format be a complete detailed description of the workflow and enable to the reader to reproduce the workflow just having the text information instead of the whole file (I opened the .ga file with textedit on mac to read the text incorporated)?

Thanks a lot

Rose

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I would be super glad for help!

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HI Rose,

I’ll try to address your questions, and throw some more options out there to consider.

I suggest keeping the entire .ga file. If that worries you, you could have both - the .ga file and a text description.

There are several things you can do with that .ga file that will make it more understandable, and more readable:

  1. Publish it on a publicly accessible Galaxy Server. This will give you a sharable link. and that way people can view the workflow inside Galaxy
  2. Upload it to Dockstore.org and or WorkflowHub.eu. I believe they both accept Galaxy Workflows.
  3. Pulbish it to Zenodo.org and get a DOI for it.

Hope this helps,
Dave C

1 Like
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Rose, just saw your other question. You could publish this on usegalaxy.eu. And you could publish it in other channels too.

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Hi Dave,

thanks a lot for your help!

So with the tex information of the .ga file (such as

{
“a_galaxy_workflow”: “true”,
“annotation”: “”,
“format-version”: “0.1”,
“name”: “Workflow 2 TST170”,
“steps”: {
“0”: {
“annotation”: “”,
“content_id”: null,
“errors”: null,
“id”: 0,

and so on), someone would be able to generate a .ga file out of this information himself and use it to import the workflow in galaxy, correct?

So I could copy and paste the text information of the .ga file in my thesis (and additionally make it publicly available at Galaxy via link)?

Thanks !

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Hi Rose.

91% (and going up!) certain that everything you said is correct.

1 Like
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Hi @tnabtaf,

may I ask you one other question regarding this matter:

Is the link for sharing a workflow stable (without publishing the workflow on the galaxy server) and could be used in a publication? (Sharing Your Galaxy Items with Other People)

Thanks
Rose

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Hi @roselucia,

A URL on usegalaxy.eu will be stable. This is one of the three big global servers. All shared links on Galaxy servers are stable for as long as the server is up. UseGalaxy.eu should be up for a long time.

Cheers, Dave C

1 Like
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Hi @tnabtaf,

after our discussion about documentation of my workflow, I used a link for sharing the workflow in my thesis (without publishing the workflow on the galaxy server). However, when I use the link today (2 years later), the following error occurs:

Please fix the following error(s):

Uncaught exception in exposed API method:

May I ask for help to fix this problem, so that the reader of my thesis can use the link to view the workflow properly on galaxy again?

Thanks for your help!

All the best,
Rose

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Hi @roselucia – Let’s continue in your new post Workflow Documentation via link