Hello Galaxy,

I'm currently working on adding some tools and am having an issue with

So, I am under the impression that BAM indexing happens automatically when a
BAM is uploaded. However there is no associated dataset_i.dat.bai file in
the file location in my local instance of galaxy.

There is however metadata which seems to be created but they are not being
linked together. What I mean to say is DELLY errors with cannot find Bam

I was curious if there is a specific way developers are suppose to work
around this? Basically we want to avoid having to provide both the BAM and
BAM index and symbolically linking a new dataset because we know you have
already created a better implementation, we just want to use it and don't
know how.

Any help is greatly appreciated,


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