Working on the arm64 porting of pipelines with @Phil Ewels - hmtnote cannot be built. github says its archived and no more updates - https://github.com/robertopreste/HmtNote/tree/master - due to HmtVar being no longer available.

HmtNote is a bioinformatics Python module and command line interface that can be used to annotate human mitochondrial variants from a VCF file, using data available on HmtVar.

and sure enough, http://www.hmtvar.uniba.it/ is very dead. Can this now be removed from the pipeline, or is there some ability to mark as deprecated?

Hi David! Yes, it is. I tried to get in touch with the developers, but there was no response from their end either. We might be replacing it with MitImpact (https://mitimpact.css-mendel.it) soon. @Tommaso Mazza, who is developing the mitodetect pipeline, is planning to make a module for it.

yes, we are making a new module in the mitodetect pipeline that will supersede hmtnote. I'll update on its implementation in our #C08CU8TU2RJ channel