BAM to FASTQ updates #2
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−249
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bridgetallen
commented
Jul 23, 2025
bridgetallen
commented
- Replaced staging file download with conditional local path handling
- Added checks for bedtools FASTQ output existence and file size
- Updated output to return a KBase report with Reads object reference
- Printed bedtools version for debugging container environment
- Improved parameter logging and error handling in do_analysis()
- Updated test BAM filename and added mock for download_staging_file
- Fixed test to assert on report_name and report_ref in returned output
- Replaced staging file download with conditional local path handling - Added checks for bedtools FASTQ output existence and file size - Updated output to return a KBase report with Reads object reference - Printed bedtools version for debugging container environment - Improved parameter logging and error handling in do_analysis() - Updated test BAM filename and added mock for download_staging_file - Fixed test to assert on report_name and report_ref in returned output
Collaborator
|
This PR is looking good! General feedback:
Beyond that, I have a few more requests:
Other than that, it looks good to me! Once these changes are made we can merge this PR to |
dakotablair
requested changes
Jul 23, 2025
lib/kb_bedtools/utils.py
Outdated
| logging.warning(f"{'@'*30} params: {params}") | ||
| print(f"{json.dumps(params)=}") | ||
| bam_file = params['bam_file'] | ||
| staging_path = bam_file if os.path.isfile(bam_file) else os.path.join("/staging/", bam_file) |
Collaborator
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Be sure your line lengths are compatible with PEP8.
added 2 commits
July 23, 2025 17:52
- adheres to PEP 8 - Imports are always put at the top of the file" - Line lengths are appropriate - Remove references to ExampleReadsApp - remove commented out lines
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