convert/from_seurat_to_h5mu

Description

Converts a Seurat file into an H5MU file.

Type

r_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
assay: [ "RNA" ]  
layers_mapping: [ "True" ]  
obs_mapping: [ "True" ]  
var_mapping: [ "True" ]  
uns_mapping: [ "True" ]  
obsm_mapping: [ "True" ]  
varm_mapping: [ "True" ]  
obsp_mapping: [ "True" ]  
varp_mapping: [ "True" ]  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/convert/from_seurat_to_h5mu/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input Seurat file
--assay	string	Name of the assay to be mapped.

Name

Type & Properties

--input

-i

file

required

--assay

string

Conversion parameters

Name	Type & Properties	Description
--layers_mapping	string	Mapping of Seurat's Layers to AnnData layers. If True, all layers will be mapped by name. If False, no layers will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--obs_mapping	string	Mapping of Seurat's observation columns to AnnData obs columns. If True, all observation columns will be mapped by name. If False, no columns will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--var_mapping	string	Mapping of Seurat's feature rows to AnnData var columns. If True, all features will be mapped by name. If False, no features will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--uns_mapping	string	Mapping of Seurat's Misc to AnnData uns. If True, all fields will be mapped by name. If False, no fields will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--obsm_mapping	string	Mapping of Seurat's Embeddings to AnnData obsm fields. If True, all fields will be mapped by name. If False, no fields will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--varm_mapping	string	Mapping of Seurat's Loadings to AnnData varm fields. If True, all fields will be mapped by name. If False, no fields will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--obsp_mapping	string	Mapping of Seurat's Graphs to AnnData obsp fields. If True, all fields will be mapped by name. If False, no fields will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--varp_mapping	string	Mapping of Seurat's Misc to AnnData varp fields. If True, all fields will be mapped by name. If False, no fields will be mapped. For custom mapping, provide a json key/value array with Seurat fields as values and AnnData fields as keys.
--x_mapping	string	A string specifying Seurat's Layer to mapped to the .X slot, If not provided, no data will be copied to the .X slot.

Name

Type & Properties

--layers_mapping

string

--obs_mapping

string

--var_mapping

string

--uns_mapping

string

--obsm_mapping

string

--varm_mapping

string

--obsp_mapping

string

--varp_mapping

string

--x_mapping

string

Outputs

Name	Type & Properties	Description
--modality	string	Name of the modality to be created.
--output -o	file required output	Output H5MU file
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--modality

string

--output

-o

file

required

output

--output_compression

string