Minor Changes to the pipeline #2
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
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
looks great, three minor suggestions:
- pandas / snakemake could be wrapped in sc-virome-scan 'base' environment (where the workflow will run from). There is env.yaml in the rootdir, though this seems to be rule specific already ?
- perhaps a --lint run (can this be combined with --dryrun) ?
- rather then flake check the name could be something related to dryrun
WardDeb
reviewed
May 16, 2023
READMD.md
Outdated
There was a problem hiding this comment.
duplicate of README.md I think ?
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
see comment on workflow, this env seems redundant with tools / kraken2.yaml ?
WardDeb
reviewed
May 16, 2023
envs/samtools.yaml
Outdated
There was a problem hiding this comment.
could this be packed with tools.yaml ?
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
Could you omit --chemistry ? Auto detection should take care of this, right ?
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
quite some potential to optimise this, though let's tackle this later.
WardDeb
reviewed
May 16, 2023
scripts/count_matrix_processing.py
Outdated
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
This function should be anonymised (e.g. os.expanduser() )
WardDeb
reviewed
May 16, 2023
There was a problem hiding this comment.
This shouldn't be in the repo I think.
WardDeb
approved these changes
May 16, 2023
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Outdated suggestions cannot be applied.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.
No description provided.