scgpt/embedding

Description

Generation of cell embeddings for the integration of single cell transcriptomic count data using scGPT.

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" ]  
obsm_gene_tokens: [ "gene_id_tokens" ]  
obsm_tokenized_values: [ "values_tokenized" ]  
obsm_padding_mask: [ "padding_mask" ]  
output: "$id.$key.output.h5mu"  
obsm_embeddings: [ "X_scGPT" ]  
pad_token: [ "<pad>" ]  
pad_value: [ -2 ]  
dsbn: [ true ]  
batch_size: [ 64 ]  
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/embedding/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input h5mu file containing tokenized gene and count data.
--modality	string	Which modality from the input MuData file to process.
--model	file required	Path to scGPT model file.
--model_vocab	file required	Path to scGPT model vocabulary file.
--model_config	file required	Path to scGPT model config file.
--obsm_gene_tokens	string	The key of the .obsm array containing the gene token ids
--obsm_tokenized_values	string	The key of the .obsm array containing the count values of the tokenized genes
--obsm_padding_mask	string	The key of the .obsm array containing the padding mask.
--var_gene_names	string	The name of the .var column containing gene names. When no gene_name_layer is provided, the .var index will be used.
--obs_batch_label	string	The name of the adata.obs column containing the batch labels. Must be provided when 'dsbn' is set to True.
--finetuned_checkpoints_key	string	Key in the model file containing the pretrained checkpoints. Only relevant for fine-tuned models.

Name

Type & Properties

--input

file

required

--modality

string

--model

file

required

--model_vocab

file

required

--model_config

file

required

--obsm_gene_tokens

string

--obsm_tokenized_values

string

--obsm_padding_mask

string

--var_gene_names

string

--obs_batch_label

string

--finetuned_checkpoints_key

string

Outputs

Name	Type & Properties	Description
--output	file required output	Path to output anndata file containing pre-processed data as well as scGPT embeddings.
--obsm_embeddings	string	The name of the adata.obsm array to which scGPT embeddings will be written.
--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

--obsm_embeddings

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--pad_token	string	The token to be used for padding.
--pad_value	integer	The value of the padding token.
--dsbn	boolean	Whether to apply domain-specific batch normalization for generating embeddings. When set to True, 'obs_batch_labels' must be set as well.
--batch_size	integer	The batch size to be used for inference

Name

Type & Properties

--pad_token

string

--pad_value

integer

--dsbn

boolean

--batch_size

integer