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

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merged 30 commits into from
Aug 21, 2024

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@dpark01 dpark01 commented Aug 19, 2024

This PR:

  • closes percolate biosample attributes to sample table in Terra #532 - percolates biosample metadata to Terra sample table in demux_deplete
  • percolates more samplesheet metadata to library table in demux_deplete
  • makes host depletion fully optional in demux_deplete (ie, works properly if all depletion database Array[File]s are empty / not specified)
  • marks the terra.upload_entities_tsv task as volatile
  • change default behavior of reports.align_and_count (used for spike-in counting) to only count proper primary mapped reads

The terra-specific bits have been tested live in a dev workspace.

@dpark01 dpark01 marked this pull request as ready for review August 20, 2024 23:38
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dpark01 commented Aug 21, 2024

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.

@dpark01 dpark01 merged commit 5623df0 into master Aug 21, 2024
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@dpark01 dpark01 deleted the dp-demux branch August 21, 2024 18:00
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percolate biosample attributes to sample table in Terra
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