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Sync development into main #750

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wants to merge 46 commits into from
Closed

Sync development into main #750

wants to merge 46 commits into from

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allyhawkins
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Continuing towards #748, this syncs all the changes in development with main. This includes a bunch of small fixes and the change to use .h5ad file extensions.

pre-commit-ci bot and others added 30 commits March 18, 2024 20:22
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate
8c65805 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3)
- [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v3.0.3...v4.0.0-alpha.8)
@jashapiro
don't update prettier, decrease frequency of updates
8d33f6d
@jashapiro
Merge pull request #732 from AlexsLemonade/pre-commit-ci-update-config
4fe5d64 
[pre-commit.ci] pre-commit autoupdate
@jashapiro
Update code to use h5ad
9dcaf38 
changed argument to predict_cellassign to make things conistent
@jashapiro
Change filenames in docs
4b0be73
@jashapiro
change variable names too
f4715c1
@jashapiro
Merge pull request #737 from AlexsLemonade/jashapiro/h5ad-output
84d5c81 
Change Anndata extension to h5ad
@allyhawkins
skip any processing for no cells after filtering
498c3a1
@allyhawkins
account for no filtered when generating qc report
75d214c
@allyhawkins
read in all columns as characters for sample metadata
f433309
@allyhawkins
check number of cols after filtering
7fa7243
@allyhawkins
don't skip filtering or processing for stubs
962c161
@allyhawkins @jashapiro
Apply suggestions from code review
4bcdecf 
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
@sjspielman
make ids match other files
e8ee05e
@allyhawkins
update indentation in filter script
1c450bb
@allyhawkins
use startsWith
25c489a
@sjspielman
Merge pull request #739 from AlexsLemonade/sjspielman/update-pool-ids
cdbac3e 
Make example ids consistent
@allyhawkins
Merge branch 'development' into allyhawkins/skip-processing-when-no-c…
2ef9e2e 
…ells
@allyhawkins
Merge pull request #738 from AlexsLemonade/allyhawkins/skip-processin…
ceee0dc 
…g-when-no-cells

Skip processing if no cells remain after empty droplet filtering
@allyhawkins
add genetic demux to channel
ecd5de5
@allyhawkins
fix double and
9dfda6d
@allyhawkins
provide genetic demux as value
71b3f63
@allyhawkins
use the correct demux options
2987439
@allyhawkins
hashedDrops not HashedDrops
233f3eb
@allyhawkins
don't convert to anndata if not enough cells
24e272b
@allyhawkins
don't run cellassign if no anndata file
9f69608
@allyhawkins
account for empty cellassign predictions
30c455e
@allyhawkins
qc report fixes
1fb9c20
@allyhawkins @jashapiro
Apply suggestions from code review
5f1c046 
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
@allyhawkins
add singler and cellassign output files to stub
296e15c
allyhawkins and others added 16 commits April 17, 2024 14:50
@allyhawkins
Merge pull request #743 from AlexsLemonade/allyhawkins/skip-cellassign
6979f6e 
Skip CellAssign if only 1 cell
@allyhawkins
Merge remote-tracking branch 'origin/development' into allyhawkins/sp…
d9eb5ba 
…ecify-demux-version
@allyhawkins
add demux methods to metadata of sce
4565e71
@allyhawkins
always use vireo unless not present
7584d4c
@allyhawkins
Revert "add genetic demux to channel"
3eab5fa 
This reverts commit ecd5de5.
@allyhawkins
Revert "provide genetic demux as value"
d32c492 
This reverts commit 71b3f63.
@allyhawkins
use correct sce and remove opt
dee63c9
@allyhawkins
Merge pull request #742 from AlexsLemonade/allyhawkins/specify-demux-…
326a04a 
…version

Account for demultiplexing without genetic demultiplexing
@allyhawkins
fix error message for feature file
62c9fd2
@allyhawkins
Merge pull request #744 from AlexsLemonade/allyhawkins/h5-feature-file
31689a1 
Account for .h5ad in output feature file
@allyhawkins
account for no cells being assigned to a sample
3a6cc4b
@allyhawkins
match order of ids and counts in metadata
ed91d33
@allyhawkins
use factor
0cf4b23
@allyhawkins
Merge pull request #745 from AlexsLemonade/allyhawkins/account-for-mi…
53fb741 
…ssing-samples

Account for no cells being assigned to a sample when demultiplexing
@allyhawkins
v0.8.0 -> v0.8.1
bef1b26
@allyhawkins
Merge pull request #749 from AlexsLemonade/allyhawkins/v0.8.1-tag-update
184d293 
Update tags to v0.8.1
sjspielman
sjspielman approved these changes Apr 23, 2024
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🚀 everything seems in place given the changes I expect, and stub check passes so that's all good enough for me!

This was referenced Apr 23, 2024
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@allyhawkins
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Closing this in favor of #752

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@allyhawkins @sjspielman @jashapiro