demux_deplete small updates #552

dpark01 · 2024-08-22T13:29:06Z

This PR:

now adds raw and cleaned read counts to Terra library table
small fix to ensure more output tsvs use unix newlines (csv.DictWriter tends to default otherwise)
fail properly on task create_or_update_sample_tables when failures are encountered in python code
bugfix for preparing sample -> library mapping when library_table_name is set to non-default value

…pelines into dp-demux

dpark01 added 10 commits August 21, 2024 09:16

fix newline outputs of csv.DictWriter invocations

49e9597

Merge branch 'dp-demux' of https://github.com/broadinstitute/viral-pi…

9fafa02

…pelines into dp-demux

add flowcell id to libraries table

b92e613

make sure to error if python code errors

ecfe7e7

oops, parameterize hardcoded library table name

362eb70

emit workflow level output files

2407c47

add read counts to library table

d9f0d38

fix parsing of wdl Pair objects are serialized

df04d03

current dxWDL doesnt like write_json, skip demux_deplete for dxWDL

842b59a

need to skip dnax build on uber-workflow that uses demux_deplete

22aa08c

dpark01 merged commit 7bbfee4 into master Aug 22, 2024
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dpark01 deleted the dp-demux branch August 22, 2024 16:56

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