because I don't want to APGL the whole repo, and I would have to do that if I used eggnog. Plus downstream mapper/visualization/enrichment analysis might be slightly easier with kofamscan output.
When I make Emily's HGT repo, I'll add a tutorial for how to do eggnog annotation on the results from the pipeline and AGPL that repo. I'll link it in the docs of this repo so people can have an example of how to use it.
~Note #24 needs to be merged before this is reviewed.~ done
Note to @mezarque, since the repo is now in Snakemake and Nextflow, and this PR touches the main pipeline, it has both. I tagged both you and Elizabeth in case you want to take a stab at reviewing the nextflow bits
because I don't want to APGL the whole repo, and I would have to do that if I used eggnog. Plus downstream mapper/visualization/enrichment analysis might be slightly easier with kofamscan output.
When I make Emily's HGT repo, I'll add a tutorial for how to do eggnog annotation on the results from the pipeline and AGPL that repo. I'll link it in the docs of this repo so people can have an example of how to use it.
~Note #24 needs to be merged before this is reviewed.~ done
~Note also remember to update the paths to the test data sets after the PR is merged in that repo. https://github.com/Arcadia-Science/test-datasets/pull/25~ done
Note to @mezarque, since the repo is now in Snakemake and Nextflow, and this PR touches the main pipeline, it has both. I tagged both you and Elizabeth in case you want to take a stab at reviewing the nextflow bits