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demux_deplete: make depletion optional, load biosample metadata to tables #551
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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. |
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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.