Taxa sqlite file name mismatch
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- Dominant language
- Nextflow
- Stars
- 14
- Forks
- 5
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Description
Description of the bug
Hello,
Thank you for developing this pipeline. Had some minor issues getting it up and running.
The taxa_sqlite files were saved as taxa.sqlite rather than taxa_sqlite.xz and same for taxa_sqlite_traverse.pkl as taxa.sqlite.traverse.pkl. They were saved in my home directory so it was possible to specify the paths with the correct names, but it would be great if you can correct the names when validating the parameters.
Additionally, the validation failed for kraken2_db when I specified just the full path, but worked when I specified the .tar.gz file with the path.
Thank you,
Ryan
Command used and terminal output
Relevant files
No response
System information
No response
Contributor guide
First steps
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Research direction
No relevant files or tests are named. Start by locating parameter validation for taxa_sqlite and kraken2_db, then verify the expected taxa filenames and whether a kraken2 directory path are accepted; done means validation handles the reported paths and names consistently.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- sqlite
- Domain
- databases, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100