Closed dpark01 closed 2 months ago
Ok this works and also as a side effect it restores the multi-library-merging functionality. It does have odd error modes if input tsv files are malformed--to do for a later date is to perhaps put some tsv validation / fail fast code up front.
This PR:
sample
table indemux_deplete
library
table indemux_deplete
demux_deplete
(ie, works properly if all depletion databaseArray[File]
s are empty / not specified)volatile
reports.align_and_count
(used for spike-in counting) to only count proper primary mapped readsThe terra-specific bits have been tested live in a dev workspace.