More improvements on TACA running Anglerfish #410
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
kedhammar
commented
Jan 30, 2024
- Use abspath for Anglerfish stderr path
- Make it possible to instantiate ONT run w/o specifying the type
- Add more info to the ONT db update subcommand
2. Make it possible to instantiate ONT run w/o specifying the type 3. Add more info the ONT db update subcommand
alneberg
reviewed
Jan 31, 2024
alneberg
reviewed
Feb 2, 2024
taca/nanopore/ONT_run_classes.py
Outdated
| self.transfer_details = CONFIG["nanopore_analysis"]["run_types"][self.run_type][ | ||
| "instruments" | ||
| ][self.instrument] | ||
| if hasattr(self, "run_type"): |
There was a problem hiding this comment.
I would change this to set self.run_type = None # Will be set in subclasses and if self.run_type is not None. I think it's easier to understand. What do you think?
There was a problem hiding this comment.
Or perhaps have run_type as a required argument to the base class as well?
d22c0f6
into
NationalGenomicsInfrastructure:master
6 checks passed
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Outdated suggestions cannot be applied.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.