Having just gone through this steps recently myself I thought I’d share quick tip. You can quickly find the absolute paths to your files that you need in the manifest file with:
find 'pwd' /path/to/your/folder/containing/fastqs .htaccess
That lists the absolute paths of all samples that you can easily copy & paste into your csv manifest file. Beats doing them one by one.
I’m sure it wouldn’t be too hard scripting the manifest creation process from files in a target folder but this is easy as well.
On another related note, is it possible to create a fastq variant detection script in the event that you don’t know where the inherited files have come from?