Propinquity output documentation. The top-level docs are here.

The phylo_input directory holds the files that are used to extract the ranked list of study+tree IDs for the phylogenetic inputs to the pipeline.

Next step: Copy the NexSON files as a snapshot. See ../phylo_snapshot/index.html for details.

Output files:

rank_collection.json is a collection JSON that is the concatenation of the collections (which where found in the phylesystem shard described in the configuration documentation.
study_tree_pairs.txt is list of the study ID + tree ID in a terse syntax that is appropriate for file names within this propinquity pipeline. These are the 1,240 trees used as inputs for this run (click any link to view a tree in a new window):
blob_shas.txt is a list of the object SHAs for the trees listed in study_tree_pairs.txt. These SHAs are used to determine if two runs of propinquity have the same phylogenetic inputs.
index.json is a JSON representation of the summaries used when writing this page.