John Eppley

I have a use case that would require a similar feature. Some of my workflows have multiple checkpoints, so --create-envs-only won't work, even with toy data, on rules that only...

Has anyone located this script or successfully updated the sortmerna databases?

I've seen similar behavior, too, and would vote for an improvement here.

PR #697 might help this somewhat. I was able to remove a little of the O(n*n) behavior from `dag.update_needrun()` which is called by `dag.postprocess()`. `update_needrun` is slow, but it normally...

I'm glad the recent DAG improvements helped. Unfortunately, in my limited time I haven't yet found any ways to speed up checkpoints specifically. To some degree, the flexibility offered by...

It sounds like you are running up against two separate problems. First the workflow isn't running to completion, and that's probably connected to the checkpoint (whether or not it's the...

Thanks for checking out our workflow. I'm sorry it's not working for either of you. I've only just begun to look into your issues, but it looks like at least...

@ttschulze , I updated the environment definition files, but I don't seem to have write access to this repository anymore. I'm no longer actively collaborating with ONT, so I guess...

@dnev1551. OK, I that's progress, but I'm sorry it's not working. It looks like the conda installer for medaka is not pulling in the correct dependencies for you. Can you...

That's odd. The versions of h5py and numpy in that environment should be compatible. I just tested on my system. What version of conda are you using? What's the output...