-
Notifications
You must be signed in to change notification settings - Fork 678
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Turn --deseq2_vst on by default #841
Comments
I second that it should be the default Also, the timeout seems unnecessary - why produce an error when things could still finish correctly? |
I also agree with this proposal. I have been processing hundreds of RNA-seq datasets and this step of the pipeline fails after 8 hours. Furthermore, since I have set automatic retries of [attempt number] * 8 hours - this would cause the pipeline to fail again after 16 hours and then again after 24 hours. Consequently, the rnaseq pipeline terminates in error and takes around 2 days to process this PCA plot, which is only for QC purposes. I think Oliver’s suggestion of having --deseq2_vst as the default option is a very good idea and should improve the pipeline substantially when processing a large number of samples. Otherwise, thanks for maintaining this great pipeline! Best, Steven |
Agree too! Will be in the next release. |
Fixed in a4be75f |
I ran rnaseq v3.8.1 on 400 samples. Failed as I got a timeout after 8hrs on
DESEQ2_QC_STAR_SALMON
process. It was still runningrlog
after 8 hours with the message:I have specified --deseq2_vst which works but i wondered if --deseq2_vst could be made default?
The text was updated successfully, but these errors were encountered: