scgpt/binning

Description

Conversion of (pre-processed) expression count data into relative values (bins) to address scale differences across sequencing batches.

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'  
modality: [ "rna" ]  
var_input: [ "id_in_vocab" ]  
n_input_bins: [ 51 ]  
output: "$id.$key.output.h5mu"  
output_obsm_binned_counts: [ "binned_counts" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/scgpt/binning/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file.
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	Mudata layer (key from .layers) to use as input data for binning. If not specified, .X is used.
--var_input	string	The name of the adata.var column containing boolean mask for vocabulary-cross checked and/or highly variable genes.
--n_input_bins	integer	The number of bins to discretize the data into. When no value is provided, data won't be binned.

Name

Type & Properties

--input

file

required

--modality

string

--input_layer

string

--var_input

string

--n_input_bins

integer

Outputs

Name	Type & Properties	Description
--output	file required output	The output h5mu file containing the binned data.
--output_obsm_binned_counts	string	The name of the adata layer to write the binned data to.
--seed	integer	Seed for random number generation.
--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_obsm_binned_counts

string

--seed

integer

--output_compression

string