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New
turns out LEVIATHAN doesn't do any kind of internal deconvolution, so a new shim script was added to the leviathan workflow to deconvolve the BX tags in the input alignments based on the [already deconvolved] MI tags.
Breaking
this has been a long time coming, but --conda was swapped for --container, meaning conda workflow dependency handling is the default now and you can opt-in to using the container-based method
.conda has been renamed .environments and will now house the conda environments and/or singularity container to simplify where harpy stores the software deps