Misleading text in rnaSPAdes "ss" parameter results in error

[sandyjmacdonald]

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"

Command used and terminal output

Relevant files

No response

System information

No response

[avani-bhojwani]

Apologies for the confusion. You would only need to type rf into that field, and it will get interpreted as --ss rf when running the pipeline.
I will update the instructions to clarify