feat: GWAS catalog top-hit DAG #33
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
There was a problem hiding this comment.
Another note, we have to merge the change to use yarn asap. This will be in #34
| @@ -0,0 +1,47 @@ | |||
| dataproc: | |||
| cluster_name: otg-tophit-gwascatalog | |||
| autoscaling_policy: otg-gwascatalog-tophit | |||
There was a problem hiding this comment.
NIT thing, but could be keep the naming consistent?
| for step in top_hits_config["nodes"]: | ||
| task = submit_gentropy_step( | ||
| cluster_name=config["dataproc"]["cluster_name"], | ||
| step_name=step["id"], |
There was a problem hiding this comment.
Just a note to me. The 'params' need to have the 'step:step_name', so the 'step_name' parameter should refer to the 'task_id' only
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This DAG handles GWAS catalog top hits independently of any other run.
It was tested and produced good outputs in 3h (slow because it only ran in the master node)
This PR requires the next PR to be merged in gentropy opentargets/gentropy#808
Co-authored with @DSuveges