species-id and ag-vampir/custom panel support

sanjaynagi / AmpSeeker

A state-of-the-art snakemake workflow for amplicon sequencing

https://sanjaynagi.github.io/AmpSeeker/

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Closed sanjaynagi closed 6 months ago

sanjaynagi commented 6 months ago

adds infrastructure for custom panels with a panel option in config.
species id notebook in workflow/notebooks/ag-vampir/
separate TOC for jupyter book if ag-vampir activated. TOC now supplied at command line.
new github actions for ag-vampir panel.

sanjaynagi commented 6 months ago

Species ID needs more work, mainly in assigning taxons. Need to discuss with malariagen folk and Eric.

but merging this now as its usable now at least and having the infrastructure merged means we can work on any other Ag-VampIR bits.