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sanger-tol / genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Add GBIF to the metadata sources #125

Open BethYates opened 3 months ago

BethYates commented 3 months ago

Description of feature

Add GBIF to the set of sources queried by the genome metadata subworkflow

BethYates commented 2 weeks ago

To close this issue you will need to download and parse a json file from GBIF and feed the parsed file into the combine metadata process in the genome_metadata subworkflow. This will most likely need it's own custom process as you actually need to fetch and parse two files to get the information we need in a 2 step process. First query https://api.gbif.org/ using genus and species https://api.gbif.org/v1/species/match?verbose=true&genus=Felis&species=catus and then use the usageKey id returned by this to do a species lookup https://api.gbif.org/v1/species/2435022 from here you can get the authorship field which is what we want to retrieve