But I did not understand what is the problem rooted in! i have some doubts on type and input-type.
First of all, please tell me how can I find the types scripts for single- and paired-end reads.
Lastly, what is the problem in your idea? How can I overcome that?
You are correct! The problem lies in the type you specified --- for single end you should use type MultiplexedSingleEndBarcodeInSequence. Also, no need to specify the format, since that format is the default format for this type. So, your new command should look like this: