Comments (1)
ressy
commented on August 22, 2024
Thinking on it more the entire check may be unnecessary. The run directory copying we use always brings over data files before text and xml, and the processor checks for completion via xml before doing anything. The only downside is extra log messages about an unfinished run. I can test this for a while with our configuration. The feature could remain but maybe with a disclaimer.
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Related Issues (20)
- Non-unicode characters crash load_csv HOT 1
- Exceptions during alignment intake should trigger admin email HOT 1
- Invalid runs not actually skipped in IlluminaProcessor.refresh HOT 2
- Migrate from Travis CI for automated testing
- The tests are atrociously inefficient and disorganized
- Box auth setup should show access error for web server log
- Handle non-unicode characters in TaskMetadata
- Box uploads should optionally set expiration on share links HOT 1
- Need a task for raw fastq.gz files HOT 1
- Need read merging task
- Project name should implicitly fill as expected in experiment spreadsheets
- Chunked Box uploader should be made fault-tolerant like the older uploader is
- Run failure should be available via Run class and the report
- Minimum versions for dependencies need to be specified
- File contents dumped to log for each Box upload
- Failed alignments should be handled HOT 2
- Task column in experiment metadata should be automatically lowercased
- Inferring expected files from sample names is just awful
- Checkpoint.txt file in Alignment directories is not parsed correctly
- Contig assembly task mis-numbers contigs
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