Hotfix/multilib annotate#109
Merged
Merged
Conversation
fix chunk offby1, add test case, make param for tuning ncontigs per annotation chunk; exclude short contigs from chunk calc"
miraep8
approved these changes
Apr 24, 2025
miraep8
left a comment
miraep8
left a comment
Contributor
There was a problem hiding this comment.
Thank you Nick! Looks great to me for now - shall we wait to merge until the latest round of annotate test apps goes through?
| outdir=temp(directory("annotation/annotation_{batch}/")), | ||
| gff=temp("annotation/annotation_{batch}.either_all_or_master.gff"), | ||
| ffn=temp("annotation/annotation_{batch}.cds.ffn"), | ||
| faa=("annotation/annotation_{batch}.cds.faa"), |
Contributor
There was a problem hiding this comment.
Should the batch level faa also be a temp file?
| gff="annotation/annotation_{batch}/data/either_all_or_master.gff", | ||
| ffn="annotation/annotation_{batch}/data/cds.ffn", | ||
| faa="annotation/annotation_{batch}/data/cds.faa", | ||
| outdir=temp(directory("annotation/annotation_{batch}/")), |
Contributor
There was a problem hiding this comment.
I think probably the outdir in the command below should be updated to make use of the $output.outdir variable?
| output: | ||
| length_file="annotation/annotation_{batch}/seqkit.length", | ||
| bed_file="annotation/annotation_{batch}/seqkit.bed", | ||
| length_file=f"{config['sample']}_metaerg.seqkit.length", |
Contributor
There was a problem hiding this comment.
These could also probably be temp files
Contributor
Author
|
Jobs are all succeeding so I'll merge |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Multiple fixes to annotation app: