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Translate the Nullarbor output into any format using Jinja2 templates

License: GNU General Public License v3.0

Python 0.54% HTML 99.39% CSS 0.07%

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Add filter for MDU IDs with an isolate identifier

Mark has asked if it would be possible to modify isolate IDs with an isolate identifier as:

2999-99999-1 as 2999-99999~1

How to add custom filters?

With these MDU specific filters, it would be a good idea to have a way of adding custom filters. Not sure how to do this yet.

add filter to identify reporting alleles in AMR

Mark suggests the following schema:

“|RPT|”                - without the surrounding quotes. Those are pipes at the start and end.

So for example:

"Results": ["aadA2|RPT|","aadB","blaCTX-M-9|RPT|","catA1","tet(A) |RPT|","aadA1*TBD*|RPT|","dfrA16*TBD*","sul1*TBD*"]

You’d probably append it after “*TBD*”, but that is not essential

The idea would be to keep a YAML file with species names, and genes/alleles that should be reported out. The file would be accessible through an environmental variable, and thus could point to whatever version of the SOP we need to run.

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