scgpt/binning
Description
Conversion of (pre-processed) expression count data into relative values (bins) to address scale differences across sequencing batches.
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. |
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. |
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 v3.0.1 \
-main-script target/nextflow/scgpt/binning/main.nf \
-params-file params.yaml Relationships
Used by
2 relationships
Current component
scgpt/binningopenpipeline v3.0.1
Uses
0 relationships
No component dependencies found.