This PR implements a sub-kingdom HGT detection approach as done in HGT-finder.
To accommodate this, the PR also:
1) renames the kingdom-level BLASTP to HGT candidates script
2) synchronizes reporting between sub-kingdom and kingdom-level prediction
3) refactors functions that are used in both scripts to an imported script (everything in functions.R has already been reviewed)
The tests are passing with Nextflow.
@elizabethmcd, can you review the nextflow changes? And anything else you're up for looking at!
@ecpierce, can you take a look at the R code?
@mezarque tagging in case you care to take a look at nextflow :)
This PR implements a sub-kingdom HGT detection approach as done in HGT-finder.
To accommodate this, the PR also: 1) renames the kingdom-level BLASTP to HGT candidates script 2) synchronizes reporting between sub-kingdom and kingdom-level prediction 3) refactors functions that are used in both scripts to an imported script (everything in
functions.Rhas already been reviewed)The tests are passing with Nextflow.
@elizabethmcd, can you review the nextflow changes? And anything else you're up for looking at! @ecpierce, can you take a look at the R code? @mezarque tagging in case you care to take a look at nextflow :)
~Note tests won't pass until https://github.com/kblin/ncbi-genome-download/issues/209 is addressed~ I've temporarily patched this with a new conda env that installs the patch.