scgpt/pad_tokenize

Description

Tokenize and pad a batch of data for scGPT integration zero-shot inference or fine-tuning.

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" ]  
input_obsm_binned_counts: [ "binned_counts" ]  
output: "$id.$key.output.h5mu"  
obsm_gene_tokens: [ "gene_id_tokens" ]  
obsm_tokenized_values: [ "values_tokenized" ]  
obsm_padding_mask: [ "padding_mask" ]  
pad_token: [ "<pad>" ]  
pad_value: [ -2 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 2.1.2 \  
  -main-script target/nextflow/scgpt/pad_tokenize/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input h5mu file of pre-processed data.
--modality	string
--model_vocab	file required	Path to model vocabulary file.
--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.
--var_input	string	The name of the adata.var column containing boolean mask for vocabulary-cross checked and/or highly variable genes.
--input_obsm_binned_counts	string	The name of the .obsm field containing the binned counts to be padded and tokenized.

Name

Type & Properties

--input

file

required

--modality

string

--model_vocab

file

required

--var_gene_names

string

--var_input

string

--input_obsm_binned_counts

string

Outputs

Name	Type & Properties	Description
--output	file required output	The output h5mu file containing obsm arrays for gene tokens, tokenized data and padding mask.
--output_compression	string	The compression type for the output 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.

Name

Type & Properties

--output

file

required

output

--output_compression

string

--obsm_gene_tokens

string

--obsm_tokenized_values

string

--obsm_padding_mask

string

Arguments

Name	Type & Properties	Description
--pad_token	string	Token used for padding.
--pad_value	integer	The value of the padding token.
--max_seq_len	integer	The maximum sequence length of the tokenized data. Defaults to the number of features if not provided.

Name

Type & Properties

--pad_token

string

--pad_value

integer

--max_seq_len

integer