workflows/integration/harmony_leiden

Description

Run harmony 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

Outputs

Name
Type & Properties
--output
file
required
output

Neighbour calculation

Name
Type & Properties
--uns_neighbors
string
--obsp_neighbor_distances
string
--obsp_neighbor_connectivities
string

Harmony integration options

Name
Type & Properties
--embedding
string
--obsm_integrated
string
--obs_covariates
string
required
multiple
--theta
double
multiple

Clustering options

Name
Type & Properties
--obs_cluster
string
--leiden_resolution
double
multiple

Umap options

Name
Type & Properties
--obsm_umap
string