Put diff files on an existing phylogenetic tree using UShER's usher sampled task with a bit of help from SRANWRP, followed by conversion of that tree to Taxonium, Newick, and Nextstrain formats. Samples' SNP distance is calculated and output as a distance matrix, and samples will be placed into clusters based on the distance.
Verified on Terra-Cromwell and miniwdl. Make sure to add --copy-input-files for miniwdl. Default inputs assume you're working with Mycobacterium tuberculosis, be sure to change them if you aren't working with that bacterium.
This repo also contains the following subworkflows:
\nFormal benchmarks have not been established, but a full run of placing 60 new TB samples on an existing 7000+ TB sample tree, conversion to taxonium and newick formats, distance matrixing, clustering finding, and creating cluster-specific Nextstrain trees executes in about five minutes on a 2019 Macbook Pro.
\nBackmasking is the least scalable part of the pipeline. The comparison itself theoretically scales n2 and once the comparison is completed, n backmasked disk files must be written to the disk. We have observed that memory problems tend to arise during the file-writing part when n\u226555 on a local machine. Runtime attributes are adjustable as task-level variables to aid with scaling on cloud backends, although we have seen the default handle 60 samples at a time without much issue.
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