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

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
tiledb_s3_no_sign_request: [ false ]  
layer: [ "log_normalized" ]  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
output_tiledb: "$id.$key.output_tiledb"  
uns_neighbors: [ "harmonypy_integration_neighbors" ]  
obsp_neighbor_distances: [ "harmonypy_integration_distances" ]  
obsp_neighbor_connectivities: [ "harmonypy_integration_connectivities" ]  
embedding: [ "X_pca" ]  
obsm_integrated: [ "X_pca_integrated" ]  
theta: [ 2 ]  
obs_cluster: [ "harmony_integration_leiden" ]  
leiden_resolution: [ 1 ]  
obsm_umap: [ "X_leiden_harmony_umap" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/workflows/integration/harmony_leiden/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file	Path to the sample. Mutually exclusive with the 'input_uri' argument.
--tiledb_input_uri	string	A URI containing the TileDB-SOMA objects. Mutually exclusive with the 'input' argument.
--tiledb_s3_region	string	Region where the TileDB-SOMA database is hosted.
--tiledb_endpoint	string	Custom endpoint to use to connect to S3
--tiledb_s3_no_sign_request	boolean	Do not sign S3 requests. Credentials will not be loaded if this argument is provided.

Name

Type & Properties

--input

file

--tiledb_input_uri

string

--tiledb_s3_region

string

--tiledb_endpoint

string

--tiledb_s3_no_sign_request

boolean

Input slots

Name	Type & Properties	Description
--layer	string	use specified layer for expression values instead of the .X object from the modality.
--modality	string	Which modality to process.

Name

Type & Properties

--layer

string

--modality

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.
--output_tiledb	file output	Output the TileDB database to the specified directory instead of adding it to the existing database.

Name

Type & Properties

--output

file

required

output

--output_tiledb

file

output

Neighbour calculation

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

Name

Type & Properties

--uns_neighbors

string

--obsp_neighbor_distances

string

--obsp_neighbor_connectivities

string

Harmony integration options

Name	Type & Properties	Description
--embedding	string	Embedding to use as input
--obsm_integrated	string	In which .obsm slot to store the resulting integrated embedding.
--obs_covariates	string required multiple	The .obs field(s) that define the covariate(s) to regress out.
--theta	double multiple	Diversity clustering penalty parameter. Can be set as a single value for all batch observations or as multiple values, one for each observation in the batches defined by --obs_covariates. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters."

Name

Type & Properties

--embedding

string

--obsm_integrated

string

--obs_covariates

string

required

multiple

--theta

double

multiple

Clustering options

Name	Type & Properties	Description
--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'.
--leiden_resolution	double multiple	Control the coarseness of the clustering. Higher values lead to more clusters.

Name

Type & Properties

--obs_cluster

string

--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