workflows/integration/totalvi_leiden

Description

Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result.

Type

nextflow_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
layer: [ "log_normalized" ]  
modality: [ "rna" ]  
prot_modality: [ "prot" ]  
output: "$id.$key.output.h5mu"  
reference_model_path: "$id.$key.reference_model_path"  
query_model_path: "$id.$key.query_model_path"  
obs_batch: [ "sample_id" ]  
max_epochs: [ 400 ]  
max_query_epochs: [ 200 ]  
weight_decay: [ 0 ]  
rna_reference_modality: [ "rna" ]  
rna_obsm_output: [ "X_totalvi" ]  
prot_reference_modality: [ "prot" ]  
prot_obsm_output: [ "X_totalvi" ]  
rna_uns_neighbors: [ "totalvi_integration_neighbors" ]  
rna_obsp_neighbor_distances: [ "totalvi_integration_distances" ]  
rna_obsp_neighbor_connectivities: [ "totalvi_integration_connectivities" ]  
prot_uns_neighbors: [ "totalvi_integration_neighbors" ]  
prot_obsp_neighbor_distances: [ "totalvi_integration_distances" ]  
prot_obsp_neighbor_connectivities: [ "totalvi_integration_connectivities" ]  
rna_obs_cluster: [ "totalvi_integration_leiden" ]  
rna_leiden_resolution: [ 1 ]  
prot_obs_cluster: [ "totalvi_integration_leiden" ]  
prot_leiden_resolution: [ 1 ]  
obsm_umap: [ "X_totalvi_umap" ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/workflows/integration/totalvi_leiden/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Path to the sample.
--layer	string	use specified layer for expression values instead of the .X object from the modality.
--modality	string	Which modality to process.
--prot_modality	string	Which modality to process.
--reference -r	file required	Input h5mu file with reference data to train the TOTALVI model.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

--modality

string

--prot_modality

string

--reference

-r

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.
--reference_model_path	file output	Directory with the reference model. If not exists, trained model will be saved there
--query_model_path	file output	Directory, where the query model will be saved

Name

Type & Properties

--output

file

required

output

--reference_model_path

file

output

--query_model_path

file

output

General TotalVI Options

Name	Type & Properties	Description
--obs_batch	string	.Obs column name discriminating between your batches.
--max_epochs	integer	Number of passes through the dataset
--max_query_epochs	integer	Number of passes through the dataset, when fine-tuning model for query
--weight_decay	double	Weight decay, when fine-tuning model for query
--force_retrain	boolean_true	If true, retrain the model and save it to reference_model_path
--var_input	string	Boolean .var column to subset data with (e.g. containing highly variable genes). By default, do not subset genes.

Name

Type & Properties

--obs_batch

string

--max_epochs

integer

--max_query_epochs

integer

--weight_decay

double

--force_retrain

boolean_true

--var_input

string

TotalVI integration options RNA

Name	Type & Properties	Description
--rna_reference_modality	string
--rna_obsm_output	string	In which .obsm slot to store the normalized RNA from TOTALVI.

Name

Type & Properties

--rna_reference_modality

string

--rna_obsm_output

string

TotalVI integration options ADT

Name	Type & Properties	Description
--prot_reference_modality	string	Name of the modality containing proteins in the reference
--prot_obsm_output	string	In which .obsm slot to store the normalized protein data from TOTALVI.

Name

Type & Properties

--prot_reference_modality

string

--prot_obsm_output

string

Neighbour calculation RNA

Name	Type & Properties	Description
--rna_uns_neighbors	string	In which .uns slot to store various neighbor output objects.
--rna_obsp_neighbor_distances	string	In which .obsp slot to store the distance matrix between the resulting neighbors.
--rna_obsp_neighbor_connectivities	string	In which .obsp slot to store the connectivities matrix between the resulting neighbors.

Name

Type & Properties

--rna_uns_neighbors

string

--rna_obsp_neighbor_distances

string

--rna_obsp_neighbor_connectivities

string

Neighbour calculation ADT

Name	Type & Properties	Description
--prot_uns_neighbors	string	In which .uns slot to store various neighbor output objects.
--prot_obsp_neighbor_distances	string	In which .obsp slot to store the distance matrix between the resulting neighbors.
--prot_obsp_neighbor_connectivities	string	In which .obsp slot to store the connectivities matrix between the resulting neighbors.

Name

Type & Properties

--prot_uns_neighbors

string

--prot_obsp_neighbor_distances

string

--prot_obsp_neighbor_connectivities

string

Clustering options RNA

Name	Type & Properties	Description
--rna_obs_cluster	string	Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'.
--rna_leiden_resolution	double multiple	Control the coarseness of the clustering. Higher values lead to more clusters.

Name

Type & Properties

--rna_obs_cluster

string

--rna_leiden_resolution

double

multiple

Clustering options ADT

Name	Type & Properties	Description
--prot_obs_cluster	string	Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'.
--prot_leiden_resolution	double multiple	Control the coarseness of the clustering. Higher values lead to more clusters.

Name

Type & Properties

--prot_obs_cluster

string

--prot_leiden_resolution

double

multiple

Umap options

Name	Type & Properties	Description
--obsm_umap	string	In which .obsm slot to store the resulting UMAP embedding.

Name

Type & Properties

--obsm_umap

string