workflows/multiomics/dimensionality_reduction
Description
Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.
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. |
PCA options
Name | Type & Properties | Description |
|---|---|---|
--obsm_pca | string | In which .obsm slot to store the resulting PCA embedding. |
--var_pca_feature_selection | string | Column name in .var matrix that will be used to select which genes to run the PCA on. |
--pca_loadings_varm_output | string | Name of the .varm key where the PCA loadings are stored. |
--pca_variance_uns_output | string | Name of the .uns key where the variance and variance ratio will be stored as a map. The map will contain two keys: variance and variance_ratio respectively. |
--pca_overwrite | boolean_true | Allow overwriting slots for PCA 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. |
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"
obsm_pca: [ "X_pca" ]
uns_neighbors: [ "neighbors" ]
obsp_neighbor_distances: [ "distances" ]
obsp_neighbor_connectivities: [ "connectivities" ]
obsm_umap: [ "X_umap" ]
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
workflows/multiomics/dimensionality_reductionopenpipeline v4.0.0