Allow inclusion of multiple species in a single genome note

[BethYates]

Description of feature

A question following the BGA genomenote session:

Stephania Sandoval: I had to leave the session a bit early today but I wanted to ask if the pipeline can be used for more than one species at a time. For example, if you have several species from the same genus and want to put them all in one genome note instead of individual notes, can that be incorporated into this pipeline? thank you!

[BethYates]

Hi Stephania, thats not something that the pipeline can do directly at the moment although we had been considering how to implement a similar use case where we would run the pipeline on different haplotypes for the same species and include the statistics and figures for both in a single genome note. I don't think it would be difficult to add the ability to process multiple species in one pipeline run, we would just need to run some of the subworkflows for each of the species and then combine all the information before passing it to a template where the placeholders are named in such a way that the species each placeholder relates to is included.

A possible work around using the existing pipeline would be to run the pipeline sequentially for each species and pass it a template that includes the output from running the pipeline with the other species. So for species "a" "b" and "c" run the pipeline for species "a" using the base template, then run the pipeline for species "b" using the output document for species "a" as the template. Finally for species "c' run the pipeline for a final time using the output document from running the pipeline on species "b". However it would be much more straightforward to expand the pipeline to allow multiple species as inputs.