How to update workflow for Dorado basecalling output

[rwilton1]

Ask away!

Hello,

I got an "project version outdated" message (bottom) when I ran wf-clone-validation today. Can you please provide or direct me to directions on how to update this? I'm not sure what file/directory it is referring to. I am running this on a linux system, and I am using Singularity (I can't use Docker on my system).

Also, although I was able to run the workflow with the outdated version, and it seemed to produce good results, I initially had some trouble getting this to work with Dorado output. I discovered I had to organize the fastqs in directories with barcode names, similar to how the Guppy output was set up. Does that sound right? I didn't see any notes about any changes regarding Dorado basecalling. ( - -Perhaps if I could get that project version updated, this would be a moot point:) )

N E X T F L O W ~ version 23.10.1 NOTE: Your local project version looks outdated - a different revision is available in the remote repository [2c04b9d884] Launching https://github.com/epi2me-labs/wf-clone-validation [kickass_newton] DSL2 - revision: fb10581c66 [master]

Thanks for your help!

[SamStudio8]

@rwiltonanl You can run nextflow pull epi2me-labs/wf-clone-validation to update the workflow (if you wish to). You may want to have a look at the CHANGELOG to see what changes may impact you https://github.com/epi2me-labs/wf-clone-validation/blob/master/CHANGELOG.md before updating.

[rwilton1]

Thanks so much! I'll definitely try this. I'm happy to see canu as an alternative assembler. Sometimes I get multimeric plasmids with flye, even if I filter out longer reads, so it will be great to have a different assembler to try.

[mattdmem]

Closing this as it looks like your question has been answered @rwiltonanl. Please do open another question if you need further information.