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Update pipeline.yml integration02
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bio-la authored Apr 19, 2024
1 parent 07e66c0 commit 45e28ae
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion tests/integration_2/pipeline.yml
Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@ rna:
# SCVI args
#-----------------------------
scvi:
seed: 1492
exclude_mt_genes: True
mt_column: mt
model_args:
Expand Down Expand Up @@ -217,7 +218,7 @@ multimodal:
# this is a minimal set of parameters that will be expected
# you can add any other param from the tutorials and they will
# be parsed alongside the others

seed: 1492
# totalvi will run on rna and prot
modalities: rna,prot
exclude_mt_genes: True
Expand All @@ -237,6 +238,7 @@ multimodal:
# you can add any other param from the tutorials and they will
# be parsed alongside the others
# leave arguments blank for default
seed: 1492
lowmem: True
# Set lowmem to True will subset the atac to the top 25k HVF.
# This is to deal with concatenation of atac,rna on large datasets which at the moment is suboptimally required by scvitools.
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