How to customize workflow page

ottojolanki · September 3, 2021, 6:44pm

Hi. I have registered my workflow onto dockstore, and now I would like to make using it as nice as possible and I have two questions about this:

I would like to be able to edit the text on Launch tab on my workflow page, how can I do this?

In the workflow main page the workflow description gets magically pulled from github, which is nice, but does not work because the links are broken. How can I add a description customized for dockstore?

Thank you,
Otto Jolanki
ENCODE-DCC

coverbeck · September 3, 2021, 7:03pm

Hi Otto,

The Workflow Launch page is currently not customizable. What sort of things do you want to have there?

You have two choices for the description:

Dockstore will by default display the description that comes from the workflow. For WDL, that means the description key in the meta section. See towards the bottom of this section.
If the descriptor doesn’t have description, then Dockstore displays the GitHub README, if present.

In practice, the WDL description is a little hard to work with because it only allows for a single line – you’ll typicaly need newline characters (\n) inline. But it’s doable. It’s a bit easier in CWL.

What sort of links are broken from the README? Do you have relative links to files in the same repo? If possible, I’d recommend trying to get the README to work, although I realize that may not be possible.

Charles

ottojolanki · September 3, 2021, 8:39pm

Hi Charles,
thanks for the quick answer. I can work with the single line in the WDL meta. Spot on, the relative links in the readme end up pointing to routes in dockstore documentation.
-Otto

ottojolanki · September 3, 2021, 8:46pm

Considering the launch section: I do not want to hardcode the docker image in the runtime description or give it as an input. I would rather use workflow options json file to define the docker image as described in your documentation here: Advanced CLI Features — Dockstore documentation
The automatically generated launch command will not work here, because of the missing --config .dockstore/config flag. Can you think of any way around this?
Is there some place instead of the launch page I can customize with the instructions to add this to the autogenerated launch commands?
Thanks!
-Otto

coverbeck · September 3, 2021, 9:39pm

Hi Otto,

I see. I logged a couple of issues for this, 4450 and 4451.

At this point, I think all you can do is update the README (or the meta/description that we talked about earlier). You could also be the first one to comment on your own workflow, something like this: Dockstore

I know neither of those solutions is ideal, but that’s all I can think of at this point.

Charles

ottojolanki · September 3, 2021, 10:08pm

Thank you, Charles for making the github issues. I will use the workarounds you suggest, and keep keeping an eye on those issues on github. Have a good weekend!
-Otto

ottojolanki · September 8, 2021, 4:37pm

Hi Charles,
I have added three of our pipelines. I tried adding the instructions as comments, but they are getting flagged as spam by the community and hidden.

I am not sure why these posts are getting flagged, maybe you can help me with figuring this out?
-Otto

dyuen · September 8, 2021, 5:08pm

Hi,
Discourse says “This new user tried to create multiple posts with links to the same domain. All posts from this user that include links should be reviewed. See the newuser_spam_host_threshold site setting.”

I approved these posts.

dyuen · September 8, 2021, 5:12pm

I also upped your trust level so you should have a higher threshold for future posts.