Open bede opened 1 year ago
handle empty before and after RIAK
ZeroDivisionError
Difficulties
*.fasta.gz
when processing empty *.fastq.gz
(easy workaround)Uploaded
state)a) Obviously we should fix viridian to handle this better, but also b) if it's spotted after RIAK we presumably dont even send to viridian?
Hi! Currently I'm keen on having ability to run e.g. empty negative control samples through the system so that they at least make it to the GPAS platform where they can be viewed in the portal, queried using APIs. It would be helpful if Viridian could treat them like any other rubbish sample with insufficient coverage – Martin is aware.
that makes sense, ok!
Thanks. I realise informatic negative controls is OTT, but as a starting point for ensuring that all neg controls auditably make it to the platform I think it's sensible, and can be optimised later.
(I need to check but) Viridian will quite possibly classify this as a fail, for too many Ns. Am right that that's fine with you so long as it completes gracefully and outputs the json?
Yes exactly : )
Should these fail validation or be skipped (with an apt warning to stderr) at upload time? Plus message for EC