1) I FTPed the tar file from the QTLseq website, then untar it
2) Based on the quick guide, we create link files that direct to the fastq files. It seems that they want to do some sort of read cleaning in the protocol. I'll try it with the reads I already cleaned with trimmomatic. If it doesn't work I'll try with the original files.
From the vignette
Naming convention *_[0-9]*__sequence.txt.gz [0-9]* : unique number; usually some number derived from lane number of flow cell  : must be assigned 1 or 2, which means “1st“ or “2nd“ of a pair-end read
3) We need to provide the cucumber 9930 reference genome