workflows/multiomics/dimensionality_reduction

Description

Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.

Type

nextflow_script

Contributors

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 1.0.1 \  
  -main-script target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf \  
  -params-file params.yaml

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.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

--modality

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.

Name

Type & Properties

--output

file

required

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_overwrite	boolean_true	Allow overwriting slots for PCA output.

Name

Type & Properties

--obsm_pca

string

--var_pca_feature_selection

string

--pca_overwrite

boolean_true

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

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