Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Initial version of sars-cov-2 variant-reporting workflow #23

Merged
merged 7 commits into from
Mar 1, 2021
Merged

Initial version of sars-cov-2 variant-reporting workflow #23

merged 7 commits into from
Mar 1, 2021

Conversation

mvdbeek
Copy link
Member

@mvdbeek mvdbeek commented Feb 22, 2021

No description provided.

@mvdbeek
Copy link
Member Author

mvdbeek commented Feb 22, 2021 •
edited
Loading

This one is failing because planemo doesn't load the "built-in" tools, like cat1. So the question is, should we change the workflow and recommend/require TS tools or change planemo to load built-in tools ?

@mvdbeek
Copy link
Member Author

mvdbeek commented Feb 22, 2021

Although maybe that's not right, planemo should load distro tools: https://github.com/galaxyproject/planemo/blob/7f27dc0f9feca7ce172f1d0f9b32cd56c667607b/planemo/galaxy/config.py#L512
Guess we need a bit more logging ...

@mvdbeek mvdbeek mentioned this pull request Feb 24, 2021
Merged
@mvdbeek
Copy link
Member Author

mvdbeek commented Feb 25, 2021

OK, for posterity, planemo was loading cat1, but only version 1.0.0, while the workflow specified version 2.0.0. Now 2.0.0 is specific to 21.01, while we were testing against master (which is release 20.09 currently). galaxyproject/planemo#1146 also loads version 2.0.0 on newer Galaxy, but for now I've downgraded to 1.0.0 in 218f0be, which is available in all galaxy instances, including 21.01 and newer

@mvdbeek mvdbeek mentioned this pull request Feb 26, 2021
Closed
mvdbeek added a commit to mvdbeek/galaxy that referenced this pull request Mar 1, 2021
@mvdbeek
Add testcase for explicit output collection step_outputs when reachin…
cb986aa 
…g max_num_jobs

This should recapitulate the error seen when running workflow tests
against galaxyproject/iwc#23.
mvdbeek added a commit to mvdbeek/galaxy that referenced this pull request Mar 1, 2021
@mvdbeek
Add testcase for explicit output collection step_outputs when reachin…
15cf05a 
…g max_num_jobs

This should recapitulate the error seen when running workflow tests
against galaxyproject/iwc#23.
@mvdbeek mvdbeek merged commit d796d17 into galaxyproject:main Mar 1, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@mvdbeek