Add data manager for clair3 models #6659
Open
+312
−0
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
| <requirement type="package" version="3.12">python</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><
There was a problem hiding this comment.
What is the known_models code doing?
There was a problem hiding this comment.
It ensures that the same model is not downloaded twice (duplicates are not allowed in the data table).
| @@ -0,0 +1,6 @@ | |||
| <tables> | |||
| <table name="clair3_models" comment_char="#" allow_duplicate_entries="False"> | |||
There was a problem hiding this comment.
I would have assumed that Galaxy automatically does not allow duplicates if allow_duplicate_entries="False".
There was a problem hiding this comment.
Alternatively the value_in_data_table might be easier?
There was a problem hiding this comment.
Nope, it lets you provide duplicate entries and then gives an error.
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Outdated suggestions cannot be applied.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.
As noted in #6547 the clair3 tool does not come with models for newer Oxford Nanopore flow cells (the R10 flow cells). These are provided by Oxford Nanopore on their Rerio page. This data manager fetches Clair3 models from that page.
NOTE: While this tool has no restrictions, the license on the Rerio page ("Oxford Nanopore Technologies, Ltd. Public License Version 1.0") is difficult to interpret and might not permit the use of the downloaded models in a commercial context. This is similar to 'research use only' tools like the BRAKER3 one (https://github.com/genouest/galaxy-tools/tree/master/tools/braker) and IUC folks need to decide on whether to include this DM in the repository, thus I have not checked the "License permits unrestricted use (educational + commercial)" box for now.
FOR CONTRIBUTOR: