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broadinstitute / viral-pipelines Public

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

Merged

dpark01 merged 30 commits intomasterbroadinstitute/viral-pipelines:masterfrom dp-demuxbroadinstitute/viral-pipelines:dp-demuxCopy head branch name to clipboard

Aug 21, 2024

+247-221

Conversation Commits30 (30)Checks Files changed

Commits

Commits on Aug 19, 2024

make depletion databases optional for demux_deplete
dpark01
committed
re-order independent code bocks
dpark01
committed
initial attempt at biosample to sample table percolation
dpark01
committed

Commits on Aug 20, 2024

oops bugfix input to multiqc cleaned
dpark01
committed
less noisy outputs
dpark01
committed
make sra_meta_prep tolerant of bam files without ".cleaned" in the filename
dpark01
committed
syntax error
dpark01
committed
restore output needed for other workflow
dpark01
committed
syntax error again
dpark01
committed
debug output
dpark01
committed
bugfix string handling
dpark01
committed
fix
dpark01
committed
bug fix
dpark01
committed
more debug
dpark01
committed
some code simplification of terra.create_or_update_sample_tables
dpark01
committed
more refactor/clean
dpark01
committed
update default
dpark01
committed
take sample original name as single value not array
dpark01
committed
cleanup, bugfix, debug
dpark01
committed
remove vestigal input
dpark01
committed
bugfix
dpark01
committed
bugfix
dpark01
committed
debug
dpark01
committed
try to fix edge case
dpark01
committed
code cleanups
dpark01
committed

Commits on Aug 21, 2024

debug
dpark01
committed
properly handle NA/NaN values in pandas dataframe
dpark01
committed
move code blocks closer together
dpark01
committed
code cleanup and reporting lines
dpark01
committed
parameterize table names
dpark01
committed

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