workflows/integration/totalvi_leiden

Description

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

Type

nextflow_script

License

MIT

Inputs

Name
Type & Properties
--id
string
required
--input
file
required
--layer
string
--modality
string
--prot_modality
string
--reference
-r
file
required

Outputs

Name
Type & Properties
--output
file
required
output
--reference_model_path
file
output
--query_model_path
file
output

General TotalVI Options

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
--rna_reference_modality
string
--rna_obsm_output
string

TotalVI integration options ADT

Name
Type & Properties
--prot_reference_modality
string
--prot_obsm_output
string

Neighbour calculation RNA

Name
Type & Properties
--rna_uns_neighbors
string
--rna_obsp_neighbor_distances
string
--rna_obsp_neighbor_connectivities
string

Neighbour calculation ADT

Name
Type & Properties
--prot_uns_neighbors
string
--prot_obsp_neighbor_distances
string
--prot_obsp_neighbor_connectivities
string

Clustering options RNA

Name
Type & Properties
--rna_obs_cluster
string
--rna_leiden_resolution
double
multiple

Clustering options ADT

Name
Type & Properties
--prot_obs_cluster
string
--prot_leiden_resolution
double
multiple

Umap options

Name
Type & Properties
--obsm_umap
string