annotate/popv

Description

Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.

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" ]  
unknown_celltype_label: [ "unknown" ]  
reference_obs_label: [ "cell_ontology_class" ]  
reference_obs_batch: [ "donor_assay" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/annotate/popv/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file.
--modality	string	Which modality to process.
--input_layer	string	Which layer to use. If no value is provided, the counts are assumed to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[input_layer]`.
--input_obs_batch	string	Key in obs field of input adata for batch information. If no value is provided, batch label is assumed to be unknown.
--input_var_subset	string	Subset the input object with this column.
--input_obs_label	string	Key in obs field of input adata for label information. This is only used for training scANVI. Unlabelled cells should be set to `"unknown_celltype_label"`.
--unknown_celltype_label	string	If `input_obs_label` is specified, cells with this value will be treated as unknown and will be predicted by the model.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--input_obs_batch

string

--input_var_subset

string

--input_obs_label

string

--unknown_celltype_label

string

Reference

Name	Type & Properties	Description
--reference	file required	User-provided reference tissue. The data that will be used as reference to call cell types.
--reference_layer	string	Which layer to use. If no value is provided, the counts are assumed to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[reference_layer]`.
--reference_obs_label	string	Key in obs field of reference AnnData with cell-type information.
--reference_obs_batch	string	Key in obs field of input adata for batch information.

Name

Type & Properties

--reference

file

required

--reference_layer

string

--reference_obs_label

string

--reference_obs_batch

string

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_compression

string

Arguments

Name	Type & Properties	Description
--methods	string required multiple	Methods to call cell types. By default, runs KNN_SCVI and SCANVI_POPV.

Name

Type & Properties

--methods

string

required

multiple