velocity/scvelo

Description

No description provided.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
layer_spliced: [ "spliced" ]  
layer_unspliced: [ "unspliced" ]  
layer_ambiguous: [ "ambiguous" ]  
output: "$id.$key.output"  
output_h5mu: "$id.$key.output_h5mu"  
log_transform: [ true ]  
n_neighbors: [ 30 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/velocity/scvelo/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input MuData file
--counts_layer	string	Name of the counts layer, if not specified, X is used.
--modality	string required	Input modality
--layer_spliced	string	Name of the layer to store the spliced abundances in. Will be used as key in the .layer attribute of the output MuData object.
--layer_unspliced	string	Name of the layer to store the unspliced abundances in. Will be used as key in the .layer attribute of the output MuData object.
--layer_ambiguous	string	Name of the layer to store the abundances in for which no fate was determined. Will be used as key in the .layer attribute of the output MuData object.

Name

Type & Properties

--input

file

required

--counts_layer

string

--modality

string

required

--layer_spliced

string

--layer_unspliced

string

--layer_ambiguous

string

Outputs

Name	Type & Properties	Description
--output	file required output	Output directory. If it does not exist, will be created.
--output_h5mu	file required output	Output mudata file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_h5mu

file

required

output

--output_compression

string

Filtering and normalization

Name	Type & Properties	Description
--min_counts	integer	Minimum number of counts required for a gene to pass filtering (spliced).
--min_counts_u	integer	Minimum number of counts required for a gene to pass filtering (unspliced).
--min_cells	integer	Minimum number of cells expressed required to pass filtering (spliced).
--min_cells_u	integer	Minimum number of cells expressed required to pass filtering (unspliced).
--min_shared_counts	integer	Minimum number of counts (both unspliced and spliced) required for a gene.
--min_shared_cells	integer	Minimum number of cells required to be expressed (both unspliced and spliced).
--n_top_genes	integer	Number of genes to keep.
--log_transform	boolean	Do not log transform counts.

Name

Type & Properties

--min_counts

integer

--min_counts_u

integer

--min_cells

integer

--min_cells_u

integer

--min_shared_counts

integer

--min_shared_cells

integer

--n_top_genes

integer

--log_transform

boolean

Fitting parameters

Name	Type & Properties	Description
--n_principal_components	integer	Number of principal components to use for calculating moments.
--n_neighbors	integer	Number of neighbors to use. First/second-order moments are computed for each cell across its nearest neighbors, where the neighbor graph is obtained from euclidean distances in PCA space.

Name

Type & Properties

--n_principal_components

integer

--n_neighbors

integer