scgpt/cross_check_genes
Description
Cross-check genes with pre-trained scGPT model.
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. |
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. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--pad_token | string | The padding token used in the model. |
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 v3.0.0 \
-main-script target/nextflow/scgpt/cross_check_genes/main.nf \
-params-file params.yaml Relationships
Used by
2 relationships
Current component
scgpt/cross_check_genesopenpipeline v3.0.0
Uses
0 relationships
No component dependencies found.