Automatic decompression of samples when uploading
seallard opened this issue · comments
Feature request from @RasmusBurge-CG
When I run cg upload for a case, it fails with an error about a single sample being compressed. Then I go and manually decompress that specific sample and try uploading again. However, it will most likely fail with a new error about another sample in the case being compressed. Repeat ad infinitum.
It would be great if decompression of samples was done automatically in the upload command. I don't want to have to manually decompress the samples one by one because it is super annoying!
Clarification
Sample files (FASTQ) are compressed after a certain amount of time. Any case where the upload fails because of sample compression is an old case.
When customers want old files re-delivered, they have to contact production via the ticketing system
Question: why can we not upload compressed files? It would be more efficient.
What are we uploading to that needs fastq files?