Merge branch 'main' into kra-logging

DendrouLab · Apr 22, 2024 · 9328dc9 · 9328dc9
2 parents 246ef5c + 73b437e
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diff --git a/docs/workflows/integration.md b/docs/workflows/integration.md
@@ -4,7 +4,7 @@ The panpipes integration pipeline implements a variety of tools to batch correct
 
 ![integration_flowchart](../img/integration_coloured.drawio.png)
 
-The flowchart indicates which tools are available for each modality out of RNA (also referred to as GEX), PROT (also referred to as ADT) and ATAC. You can run as many of these tools as you choose and then you can run `panpipes integration make merge_batch_correction` to create a final object containing one reduced dimension representation and one nearest neighbor graph per modality. This can be used as input to the clustering pipeline.
+The flowchart indicates which tools are available for each modality out of RNA (also referred to as GEX), PROT (also referred to as ADT) and ATAC. You can run as many of these tools as you choose and then you can run `panpipes integration make merge_integration` to create a final object containing one reduced dimension representation and one nearest neighbor graph per modality. This can be used as input to the clustering pipeline.
 
 ## Steps to run
 
@@ -16,7 +16,7 @@ The flowchart indicates which tools are available for each modality out of RNA (
 3. Use pipeline outputs to decide on the best batch correction method
 4. Edit the integration pipeline yml with your preferred batch
     correction
-5. Run `panpipes integration make merge_correction`
+5. Run `panpipes integration make merge_integration`
 
 ## Expected structure of MuData object
 

diff --git a/tests/integration_1/pipeline.yml b/tests/integration_1/pipeline.yml
@@ -70,6 +70,7 @@ rna:
   # SCVI args
   #-----------------------------
   scvi:
+    seed: 1492
     exclude_mt_genes: True
     mt_column: mt
     model_args:
@@ -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
@@ -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.

diff --git a/tests/integration_2/pipeline.yml b/tests/integration_2/pipeline.yml
@@ -70,6 +70,7 @@ rna:
   # SCVI args
   #-----------------------------
   scvi:
+    seed: 1492
     exclude_mt_genes: True
     mt_column: mt
     model_args:
@@ -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
@@ -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.