clarifying issues - #34
Merged
Merged
Conversation
Contributor
There was a problem hiding this comment.
Pull request overview
Updates README.md to improve clarity and readability of the project overview and usage documentation.
Changes:
- Clarifies the project motivation and expands the explanation of cluster-specific scripts.
- Updates and expands the “Pipeline Steps” section (adds an optional phage-gene annotation step and more assembly detail).
- Standardizes heading capitalization and refines the “System Nuances” section (adds more detailed HPC notes and introduces a new “Ways To Modify…” section header).
Suppressed comments (2)
README.md:161
- This sentence is grammatically incorrect ("uses PBS for scheduling a
/g/datadrive" is missing "and has a"). Tweaking the wording also makes the array-job constraint clearer.
Gadi uses PBS for scheduling a `/g/data` drive that is used for temporary storage. Gadi does not allow array jobs with more than 10 jobs, so
we have to run each step separately.
README.md:168
- There are multiple consecutive blank lines after this new heading, which adds unnecessary vertical whitespace and makes the section look unfinished.
# Ways To Modify atavide lite Output
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+52
to
+54
| 7. [Optional] We annotate the phage genes using PHROGs, and create a summary of those genes | ||
| 8. Use megahit to assemble the reads. We are fans of complete cross-assembly, but this takes time and resources, but megahit | ||
| provides an option that allows us to continue where it left off, so after a few days or weeks the assembly finishes. |
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
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.
Updating the readme