wrappers/multiomics/neighbors_leiden_umap
Description
Performs neighborhood search, Leiden clustering and UMAP on an integrated
embedding, running either the GPU (rapids-singlecell) or the CPU (scanpy)
variant of the whole workflow, selected with --device_type.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Path to the input H5MU file. |
--obsm_input | string required | The key of the embedding to use as input. |
--modality | string | Which modality to process. |
Compute
Name | Type & Properties | Description |
|---|---|---|
--device_type | string | Which implementation to run: the GPU (rapids-singlecell) variant or the CPU (scanpy/squidpy) variant of the component. Selecting `gpu` requires a CUDA-capable GPU; the component errors out if none is available (there is no automatic fallback to CPU). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Destination path to the output. |
Neighbour calculation
Name | Type & Properties | Description |
|---|---|---|
--uns_neighbors | string required | In which .uns slot to store various neighbor output objects. |
--obsp_neighbor_distances | string required | In which .obsp slot to store the distance matrix between the resulting neighbors. |
--obsp_neighbor_connectivities | string required | In which .obsp slot to store the connectivities matrix between the resulting neighbors. |
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 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. When not specified, UMAP will not be executed. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
device_type: [ "gpu" ]
output: "$id.$key.output.h5mu"
leiden_resolution: [ 1 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_rapids.git \
-revision v0.1.3 \
-main-script target/nextflow/wrappers/multiomics/neighbors_leiden_umap/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
wrappers/multiomics/neighbors_leiden_umapopenpipeline_rapids v0.1.3