Launch pipeline gives String instead of Number
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- Dominant language
- Python
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Description
Description of the bug
Not sure what the cause is for this so it this report might not be on the correct repo. I tried the online launch feature on the website for the mag-pipeline. For one of the paramters, the "max_unbinned_contigs", the output params.json puts the integer inside quotes:
{
"min_length_unbinned_contigs": 100000,
"max_unbinned_contigs": "0",
"binqc_tool": "checkm"
}
this results in an error when running the pipeline:
ERROR: Validation of pipeline parameters failed!
* --max_unbinned_contigs: expected type: Number, found: String (0)
The html field seems to be aware that it's a number so not sure where the error occurs.
Command used and terminal output
No response
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the online launch feature that generates params.json and trace how the max_unbinned_contigs value is serialized. Compare it with min_length_unbinned_contigs and verify the generated parameters pass pipeline validation with max_unbinned_contigs represented as a number rather than a quoted string.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100