Kiran V Garimella
Kiran V Garimella
McCortex loads all the graphs into memory before joining them, and yes, this can be a bit slow. I think what you've outlined *would* be faster, but it's not clear...
Wow, one read? Is this a test BAM file or real data?
This is an interesting one. Thinking ahead to amplicon sequencing, there will certainly be cases where we parallelize over chromosomes and some will have no data. So it looks like...
I looked into this, and it's not really clear to me that NCRF is meant for use in the way we're expecting. It takes as input a fasta file, and...
Yeah, given that we're getting better and better at running automated analyses, separating these functionalities into two separate workflows seems quite sensible to me.
I second this. I'll also suggest that we add [noise-cancelling repeat finder](https://github.com/makovalab-psu/NoiseCancellingRepeatFinder) (NCRF) to the mix.
Yeah, I've looked into NCRF and am no longer sure it'll easily go into our workflows.
Maybe we should consider auto-removing stale branches. For the Dockstore branches, this is actually part of our release process to Terra - it's where all the WDL imports get rewritten...
@kvg to investigate rewriting the release process to not rewrite imports anymore, cutting down on number of branches we need to keep around.
I'm going to move lr-seanken out of this repo and keep it somewhere else to return to later.