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Misleading text in rnaSPAdes "ss" parameter results in error

#23Closedsandyjmacdonald 创建于 2024-11-13
bug
S
sandyjmacdonaldcommented
### Description of the bug In the rnaSPAdes configuration when setting the pipeline up, there is some text that says: ``` Set strand-specific type for rnaSPAdes. Use `--ss rf` when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and `--ss fr` otherwise (forward). ``` To me, this suggests that you should enter `--ss rf` when configuring that parameter, however this results in the error below. The parameter entered here should just be `rf` or `fr`. See screenshot below to illustrate where we went wrong... ``` spades.py: error: argument --ss: expected one argument ``` I would suggest clarifying the text by changing "Use --ss rf when first read in pair..." to be "Use rf when first read in pair" ![Image](https://github.com/user-attachments/assets/93e78189-1aa7-4b76-a593-d58506a217e9) ### Command used and terminal output ```console ``` ### Relevant files _No response_ ### System information _No response_
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