Using Galaxy main usegalaxy.org) I have been happily runnning Salmon followed by Deseq2 to get normalized counts on some small RNAseq data. Up until Mon 21 May 07:37:49 PM(UTC) all ran just fine. But the next time I tried to use Deseq2 on a different Salmon set at 8:20:28, I got an empty file as a result (0 lines). Repeated rerun of Salmon and deseq2 have resulted in the same. I have searched through every parameter, and have not done anything differently, and have reached the end of my own troubleshooting capabilities.
Weirdly, if I rerun that Deseq2 job from Mon 21 May 07:37:49 PM(UTC), it returns the data just fine like it did the first time. It seems like there is something changed about how Salmon output happens now, since my 'old' Salmon outputs (from earlier yesterday) work in Deseq2 but my newer Salmon outputs won't work, and give 0 lines after running Deseq2.
Thanks for any help you can give.