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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Automatic decompression of samples when uploading #3319

Open seallard opened 1 month ago

seallard commented 1 month ago

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!

seallard commented 1 month ago

Question: why can we not upload compressed files? It would be more efficient.

henrikstranneheim commented 1 month ago

What are we uploading to that needs fastq files?