Update readme #22
Update readme #22
Conversation
WalkthroughAh, listen up, my culinary comrades! The latest updates to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant GATK
participant DXTool
User->>DXTool: Request data object
DXTool-->>User: Provide data object based on version
User->>GATK: Input data for CNV calling
GATK-->>User: Return results
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Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: ASSERTIVE
📒 Files selected for processing (1)
README.md(1 hunks)
🔇 Additional comments (1)
README.md (1)
68-73: Magnifique! The version-specific command examples are perfectly seasoned!
Ah, mes amis! The separation of commands by toolkit version is chef's kiss - absolutely brilliant! The clear labelling of version constraints (< v0.386.0 and >= v0.387.0) helps users pick the right recipe for their kitchen setup.
| > *dx-toolkit < v0.386.0* | ||
| > | ||
| > `$ dx find data --path project:folder --name ".*bam$|.*bai$" --name_mode "regexp" --json | jq -r '.[].id' | sed 's/^/-ibambais=/g'` | ||
| > | ||
| > *dx-toolkit >= v0.387.0* | ||
| > |
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🧹 Nitpick (assertive)
Consider adding a note about command output format consistency
Listen carefully, mon petit chou! While both commands produce the same delightful output, it would be très bon to add a small note confirming that both commands will generate identical output format. Just like ensuring your soufflé rises the same way every time!
*dx-toolkit >= v0.387.0*
+Note: Both commands generate identical output format suitable for the -ibambais parameter.
+
where `<project>` and `<folder>` are the project and path to the bam files, respectively.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| > *dx-toolkit < v0.386.0* | |
| > | |
| > `$ dx find data --path project:folder --name ".*bam$|.*bai$" --name_mode "regexp" --json | jq -r '.[].id' | sed 's/^/-ibambais=/g'` | |
| > | |
| > *dx-toolkit >= v0.387.0* | |
| > | |
| > *dx-toolkit < v0.386.0* | |
| > | |
| > `$ dx find data --path project:folder --name ".*bam$|.*bai$" --name_mode "regexp" --json | jq -r '.[].id' | sed 's/^/-ibambais=/g'` | |
| > | |
| > *dx-toolkit >= v0.387.0* | |
| > | |
| Note: Both commands generate identical output format suitable for the -ibambais parameter. |
💡 Codebase verification
Attention! This recipe needs a cautionary note, mes amis!
The documentation shows two different command styles for dx-toolkit versions, but like a soufflé without proper instructions, it's missing the crucial details! The newer version (>=v0.387.0) appears to be missing its command example entirely, leaving our users hanging mid-recipe!
- The README shows a command for dx-toolkit < v0.386.0
- The section for dx-toolkit >= v0.387.0 is empty, with only a note about project and folder parameters
- There's an alternative
dx apicommand shown, but without version context
Like any good recipe, we must ensure completeness and clarity. This documentation needs the complete command for the newer version to ensure our users can execute their tasks perfectly, regardless of their dx-toolkit version.
🔗 Analysis chain
Verify the command compatibility across dx-toolkit versions
Mon dieu! We must ensure our recipe works perfectly across all kitchens! Let's verify these commands work as documented for the specified versions.
Let me explain, mon ami! Like checking if we have all ingredients before starting our recipe, we need to find any documentation about these version changes. We'll search for version notes, configuration files, and any documentation that might explain the difference between these commands. This will help us ensure our recipe is perfectly seasoned for all versions!
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify dx-toolkit version-specific commands
# Check if README mentions all supported dx-toolkit versions
rg -A 2 "dx-toolkit.*v0\." README.md
# Look for any other dx command examples that might need version-specific variants
rg "dx\s+(api|find|run|select|upload)" README.md
Length of output: 736
Script:
#!/bin/bash
# Let's check if there's any documentation or changelog about the dx-toolkit version changes
rg -i "version|changelog|release" README.md
# Search for any dx API documentation files that might explain the changes
fd -t f -e md -e txt . | xargs rg -l "dx-toolkit|dx api|dx find"
# Look for any configuration files that might specify dx-toolkit version requirements
fd "package|requirements|setup|config" -e json -e txt -e yml -e yaml | xargs cat
Length of output: 205
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Reviewed 1 of 1 files at r1, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @jethror1)
dx find datawith dx-toolkit > 0.387.0This change is