Update/input assure to accommodate changes in locidex mlst.json allele reports #28
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
… Locidex mlst.json report format
|
…rom ci.yml and add to modules.conf
apetkau
requested changes
Aug 20, 2024
There was a problem hiding this comment.
This is amazing work @kylacochrane 😄 . Thanks so much for all these changes. I have only a few comments.
sgsutcliffe
approved these changes
Aug 20, 2024
|
@sgsutcliffe That would be fantastic! Creating an issue for this would be really helpful. I agree that it is important to add some information about the |
apetkau
approved these changes
Aug 21, 2024
| @@ -3,6 +3,15 @@ | |||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | |||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | |||
|
|
|||
| ## [0.3.0] - 2024-08-21 | |||
There was a problem hiding this comment.
Could you also add the link to this tag like the other releases, even if the tag isn't created yet (in anticipation of when we release)?
There was a problem hiding this comment.
done here: cf5248e
😃
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Outdated suggestions cannot be applied.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 PR upgrades the version of the
locidex/mergemodule tolocidex:0.2.2in the container directive. The new version of locidex includes changes to the formatting of generatedmlst.jsonallele report files (such as those outputted from Mikrokondo).To ensure compatibility, the
input_assuremodule and python script have been updated to accommodate these changes in themlst.jsonallele reports. The test data has also been updated to reflect the newmlst.jsonformat. All pipeline tests are passing.New
mlst.jsonformatting:Additionally, container directives and closures have been aligned with the
phac-nml/pipeline-standardsas outlined in the Module Software Requirements and Container RegistresPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.