“BTW, it doesn’t bother me, but I think there is a problem with the column names in the NextClade tables: https://galaxy.hpc.ut.ee/datasets/8fb1cd32e9c26adb/display/?preview=True. There is a mismatch between column name and content from some point (and in total one less column name than there are columns), I think the column name “insertionsmissing” should actually be two column names “insertions” and “missing”"
scorpioseems to specifically related to identifying VOCs based on constellations of mutations.
--ushermode, it will use
lineageTree.pbfrom the paangoLEARN data as the model (tree) - https://github.com/cov-lineages/pangolin/blob/4a4f5ec390efba89524ac6f4365981199607c1cb/pangolin/command.py#L295
GTis not worth keeping it seems to me.
ALT_FREQto the much more common
AFto enhance interoperability with other tools.
Got a fun one here for workflow version pinning breaking because the version of Python was not specified: peterjc/pico_galaxy#37
What I think is happening is my old workflow (on the Tool Shed) is pointing at an old Python-2-only version of my RXLR tool, which breaks under a modern Python-3 based Galaxy. The RXLR tool itself was updated for Python 3, but the workflow was not updated to point at this.