fairly new to manipulating scripts, and I would appreciate some guidance on the builds and parameters yamls.
followed a tutorial to create a custom profile in my_profiles, and edit the builds yaml.
im not exactly sure which entries are required, and which are optional. and where do I adjust the parameters for all the tools (for example, I do not want any entries filtered, so I dont really need and ‘exclude’ parameters). I imagine that if i do not specify some parameters, it defaults to …default values.
as an example,
I uploaded entries onto GISAID, so that will be my starting point for this nextstrain analysis. So i’d appreciate a guide from how to download from there. I know there are several ways (tar, or extracted fasta and metadata), but not sure if there is a difference between them. I’ll have roughly 80 entries, and do need to filter them in any way. All from the same country, just different states. end result should be an auspice map showing strains in each area.
The error message I get has something to do with all entries being filtered out due to ambiguous date in any. I imagine because of default values, and that my dates when submitted to GISAID were dd-mm-yyyy, whereas nextstrain needs it to be yyyy-mm-dd?
tldr; what the minimum i need in builds yaml, and where do i change values in parameter, like removing the need for filtering.