workflows/integration/harmony_leiden
Description
Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.
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. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Destination path to the 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. |
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. Specify for each variable in group.by.vars. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters." |
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. |
Umap options
Name | Type & Properties | Description |
|---|---|---|
--obsm_umap | string | In which .obsm slot to store the resulting UMAP embedding. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
id: "run"
layer: [ "log_normalized" ]
modality: [ "rna" ]
output: "$id.$key.output.h5mu"
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" ]
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 1.0.2 \
-main-script target/nextflow/workflows/integration/harmony_leiden/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/integration/harmony_leidenopenpipeline 1.0.2