theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
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add task for pangolin v4 #121

Closed kapsakcj closed 2 years ago

kapsakcj commented 2 years ago

v4 hasn't been released just yet, but would be good to have a task ready to go when the time comes

will require:

docs on usage here: https://cov-lineages.org/resources/pangolin/usage.html Looks to be similar to v3

docs on output format here: https://cov-lineages.org/resources/pangolin/output.html

kapsakcj commented 2 years ago

working on this dev branch https://github.com/theiagen/public_health_viral_genomics/tree/cjk-pangolin-v4-dev

added task pangolin4, but need to update all workflows that call the task.

task_taxonID.wdl passes miniwdl check but needs to be tested with real data