Update irma recipe to version 1.1.4 #51522
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request includes several changes across different patches related to the IRMA project. The first patch modifies the error handling for checking the writable status of the output directory, shifting from an abort mechanism to logging a warning message. The second patch focuses on script modifications, including simplifying variable assignments for various binaries, updating how the Rscript executable is referenced, introducing new variables for Perl scripts, and adding conditional logic for sourcing a configuration file. Additionally, it refines string checks and command checks for consistency. The third patch updates the Suggested labels
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/irma/irma-check-dir-writable.patch (1)
6-8: Approve change with minor correctionThe shift from aborting to warning is noted. This change allows for more flexible error handling, which aligns with the version update to 1.1.4. However, there's a small typo in the warning message.
Consider correcting the typo in the warning message:
- timestamp "WARNING: output directory may not writable: $destination_directory" + timestamp "WARNING: output directory may not be writable: $destination_directory"recipes/irma/irma-fix-bin-cmds.patch (3)
21-22: New variables MERGESAMPAIRS and FASTQ_CONVERTER added.The addition of these variables improves code organization. Consider adding comments to explain the purpose and usage of these new variables for better maintainability.
27-35: Good addition of user config file support, but consider adding safeguards.The ability to load a user config file enhances flexibility. However, consider the following suggestions:
- Add documentation on what can be configured in 'irma_config.sh'.
- Implement safeguards to prevent unintended overrides of critical variables.
- Consider validating the loaded configurations to ensure they don't break the script's functionality.
Missing Required Binaries in PATH
The following binaries are not available in the system PATH:
- parallel
- samtools
- blat
- minimap2
- Rscript
Please install these binaries or ensure they are included in the PATH on all target environments to maintain script portability and functionality.
🔗 Analysis chain
Line range hint
3-13: Simplified variable assignments look good, but verify PATH assumptions.The changes to PARALLEL, SAMTOOLS, BLAT, MM2, RSCRIPT, and BASH variables improve portability and readability. However, ensure that these binaries are available in the system PATH on all target environments.
Run the following script to verify the availability of the required binaries:
Source URL is accessible and updated correctly.
The new source URL returns a successful HTTP status code (200), confirming its accessibility and correctness.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the accessibility and content of the new source URL # Test: Check if the URL is accessible and download the zip file curl -I https://wonder.cdc.gov/amd/flu/irma/flu-amd-202402.zipLength of output: 229
Script:
#!/bin/bash # Description: Verify the accessibility of the new source URL # Test: Check if the URL returns a successful HTTP status code (200) curl -s -o /dev/null -w "%{http_code}" https://wonder.cdc.gov/amd/flu/irma/flu-amd-202402.zipLength of output: 99
recipes/irma/irma-fix-bin-cmds.patch (2)
35-35: Improved string check for LFASTM.The change from
! -zto-nfor checking if LFASTM is non-empty is a good practice. It's more idiomatic and slightly more efficient in shell scripting.
39-46: Simplified command check for pigz looks good.The changes improve readability and portability. However, ensure that 'pigz' is available in the system PATH on all target environments where it's expected to be used.
Run the following script to verify the availability of pigz and gzip:
#!/bin/bash # Description: Check if pigz and gzip are available in PATH for cmd in pigz gzip; do if command -v "$cmd" &> /dev/null; then echo "$cmd is available" else echo "Warning: $cmd is not found in PATH" fi done
wm75
changed the title
Updated IRMA (1.0.3 -> 1.1.4)