Dumping this here quickly and we can integrate later(if possible make some simple tests and put in new release coming up)
The linked gist just takes a MiSeq run path and finds *.fastq.gz and then extracts sample name from each of the found files by splitting on _ and taking the first element of the list.
Then creates a directory with that name and symlinks or copys the fastq.gz into that directory
https://gist.github.com/necrolyte2/fbd9188edbf58ee57a60e36771c75d78
It has become apparent that this is needed
Dumping this here quickly and we can integrate later(if possible make some simple tests and put in new release coming up)
The linked gist just takes a MiSeq run path and finds *.fastq.gz and then extracts sample name from each of the found files by splitting on
_
and taking the first element of the list. Then creates a directory with that name and symlinks or copys the fastq.gz into that directory