Marius van den Beek
Marius van den Beek
I would really appreciate it if we didn't need one instance per workflow. To make it simpler, we could update all workflows by dropping `if config.updated_repos.get(workflow.path) or kwds.get("engine") == "external_galaxy":`....
> This API will allow us to just register a validated tool request in the database and let the job creation process happen within a Celery task. That's also a...
Unit tests look relevant ?
Clearing the milestone, as a bug this can go in whenever
@natefoo can you take a look at this ?
Just to record my exchange with @natefoo here, I am on board with this change (minus `if (self.auto_install or install) and not os.path.exists(cache_path):`, that should be an unreachable condition after...
What Nate is doing here is correct and fixing a bug. So the test assumption seems to be wrong but I haven't wrapped my head around exactly what the test...
Fix the test is all
The docker container for this tool has been published via https://github.com/BioContainers/multi-package-containers/pull/3640 and it might take a day or so to appear on cvmfs: ``` ❯ docker run quay.io/biocontainers/mulled-v2-b8c00919e78e310f5965a5971fdc4280dbc6cc1c:8560a6b7521ee456cdc1c45196aae3f3236a29bc-0 datasets WARNING:...
> * It also exposes `--outBAMsortingBinsN` and `--winAnchorMultimapNmax` params which already exist in STAR. I don't think `--outBAMsortingBinsN` should be a user option, can you calculate reasonable value for that...