Scvelo

Info

ID: scvelo
Namespace: velocity

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -main-script target/nextflow/velocity/scvelo/main.nf \
  --help

Run command

Example of params.yaml
# Inputs
input: # please fill in - example: "path/to/file"

# Outputs
# output: "$id.$key.output.output"
# output_compression: "gzip"

# Filtering and normalization
# min_counts: 123
# min_counts_u: 123
# min_cells: 123
# min_cells_u: 123
# min_shared_counts: 123
# min_shared_cells: 123
# n_top_genes: 123
log_transform: true

# Fitting parameters
# n_principal_components: 123
n_neighbors: 30

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/velocity/scvelo/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name Description Attributes
--input Velocyto loom file. file, required

Outputs

Name Description Attributes
--output Output directory. If it does not exist, will be created. file, required
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"

Filtering and normalization

Arguments for filtering, normalization an log transform (see scvelo.pp.filter_and_normalize function)

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

Fitting parameters

Arguments for fitting the data

Name Description Attributes
--n_principal_components Number of principal components to use for calculating moments. integer
--n_neighbors 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. integer, default: 30

Authors

  • Dries Schaumont (maintainer)