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v0.3.2 #368

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Jun 24, 2024
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a3420fd
Update to v0.3.0 (#237)
sjfleming Aug 6, 2023
02dd763
Add Nature Methods citation and update docs
sjfleming Aug 7, 2023
da9fabb
Merge branch 'master' into dev
sjfleming Aug 28, 2023
e358888
Add WDL input to set number of retries. (#247)
kshakir Oct 31, 2023
7a834a4
Move hash computation so that it is recomputed on retry, and now-inva…
alecw Oct 31, 2023
cf71148
Bug fix for WDL using MTX input (#246)
sjfleming Oct 31, 2023
322971d
Memory-efficient posterior generation (#263)
sjfleming Oct 31, 2023
12b4758
Fix posterior and estimator integer overflow bugs on Windows (#259)
sjfleming Oct 31, 2023
be36006
Move from setup.py to pyproject.toml (#240)
sjfleming Oct 31, 2023
084194b
Fix bugs with report generation across platforms (#302)
sjfleming Oct 31, 2023
a4da38a
Merge branch 'master' into dev
sjfleming Oct 31, 2023
97c1d40
Fix major bug in v0.3.1: negative counts (#347)
sjfleming Apr 11, 2024
d0cfc36
Merge branch 'master' into dev
sjfleming Apr 19, 2024
578c214
Tweak readme appearance
sjfleming Apr 19, 2024
80514f0
Add newer Cell Ranger feature types (#339)
jpintar Apr 22, 2024
72e6a3f
Fix test_elbo bug when retrying with more memory from checkpoint (#345)
alecw Apr 22, 2024
a71e183
Retry: prevent ZeroDivisionError if initial test ELBO is the best tes…
alecw Apr 23, 2024
f3c8865
Merge branch 'master' into dev
sjfleming Jun 21, 2024
2c3dbe8
Azurize CellBender to run on ToA (#367)
aawdeh Jun 24, 2024
569b7b1
Updates to benchmarking scripts
sjfleming Jun 24, 2024
31130fd
Update documentation in anticipation of v0.3.2
sjfleming Jun 24, 2024
1198d8f
Update wdl for benchmarking compatibility
sjfleming Jun 24, 2024
87f33e1
Merge branch 'dev' of github.com:broadinstitute/CellBender into dev
sjfleming Jun 24, 2024
d7d228b
Bump version to v0.3.2
sjfleming Jun 24, 2024
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Add newer Cell Ranger feature types (#339)
In Cell Ranger 7+, there is a longer list of features one can specify in `cellranger multi`. These are added here to the list of allowed features.
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jpintar authored Apr 22, 2024
commit 80514f06aea41795486ee0caea07a41b67498f90
12 changes: 10 additions & 2 deletions cellbender/remove_background/cli.py
Original file line number Diff line number Diff line change
@@ -117,14 +117,22 @@ def validate_args(args) -> argparse.Namespace:
args.fpr = fpr_list_correct_dtypes

# Ensure that "exclude_features" specifies allowed features.
# As of CellRanger 6.0, the possible features are:
# As of CellRanger 7.2, the possible features are:
# Gene Expression
# Antibody Capture
# CRISPR Guide Capture
# Custom
# Peaks
# Multiplexing Capture
# VDJ
# VDJ-T
# VDJ-T-GD
# VDJ-B
# Antigen Capture
allowed_features = ['Gene Expression', 'Antibody Capture',
'CRISPR Guide Capture', 'Custom', 'Peaks']
'CRISPR Guide Capture', 'Custom', 'Peaks',
'Multiplexing Capture', 'VDJ', 'VDJ-T',
'VDJ-T-GD', 'VDJ-B', 'Antigen Capture']
for feature in args.exclude_features:
if feature not in allowed_features:
sys.stdout.write(f"Specified '{feature}' using --exclude-feature-types, "