scgpt/cross_check_genes

Description

Cross-check genes with pre-trained scGPT model.

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" ]  
output: "$id.$key.output.h5mu"  
output_var_filter: [ "id_in_vocab" ]  
pad_token: [ "<pad>" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.1 \  
  -main-script target/nextflow/scgpt/cross_check_genes/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input h5mu file containing of pre-processed data.
--modality	string	The modality key of the MuData object containing the RNA AnnData object.
--vocab_file	file required	Model vocabulary file path.
--input_var_gene_names	string	The name of the adata.var column containing gene names. By default the .var index will be used.
--var_input	string	.var column containing highly variable genes. If provided, will only cross-check HVG filtered genes with model vocabulary.

Name

Type & Properties

--input

file

required

--modality

string

--vocab_file

file

required

--input_var_gene_names

string

--var_input

string

Outputs

Name	Type & Properties	Description
--output	file required output	The output cross-checked anndata file.
--output_var_filter	string	In which .var slot to store a boolean array corresponding to which observations should be filtered out based on HVG and model vocabulary.
--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_var_filter

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--pad_token	string	The padding token used in the model.

Name

Type & Properties

--pad_token

string