velocity/scvelo

Description

No description provided.

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
log_transform: [ true ]  
n_neighbors: [ 30 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/velocity/scvelo/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Velocyto loom file.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output directory. If it does not exist, will be created.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--output

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