convert/from_h5mu_or_h5ad_to_tiledb

Description

Convert a MuData or AnnData object to tiledb. Currently, transcriptome and protein modalities are supported.

NOTE: The functionality provided by this component is experimental and may be subject to change.

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'  
rna_modality: [ "rna" ]  
rna_modality_output: [ "rna" ]  
prot_modality_output: [ "prot" ]  
obs_index_name_output: [ "cell_id" ]  
rna_var_index_name_output: [ "rna_index" ]  
rna_raw_layer_output: [ "X" ]  
rna_normalized_layer_output: [ "log_normalized" ]  
rna_var_gene_names_output: [ "gene_symbol" ]  
prot_var_index_name_output: [ "prot_index" ]  
prot_raw_layer_output: [ "X" ]  
prot_normalized_layer_output: [ "log_normalized" ]  
tiledb_dir: "$id.$key.tiledb_dir"  
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_h5mu_or_h5ad_to_tiledb/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	Input AnnData or MuData file. When an AnnData file is provided, it is automatically assumed to contain transcriptome counts.

Name

Type & Properties

--input

file

required

RNA modality

Name	Type & Properties	Description
--rna_modality	string	The name used for the RNA modality. Used when input file is a MuData object.
--rna_raw_layer_input	string required	Location of the layer containing the raw transcriptome counts. Layers are looked for in .layers, except when using the value 'X'; in which case .X is used.
--rna_normalized_layer_input	string required	Location of the layer containing the normalized counts. Layers are looked for in .layers, except when using the value 'X'; in which case .X is used.
--rna_var_gene_names_input	string	Column in .var that provides the gene names. If not specified, the index from the input is used.

Name

Type & Properties

--rna_modality

string

--rna_raw_layer_input

string

required

--rna_normalized_layer_input

string

required

--rna_var_gene_names_input

string

Protein modality

Name	Type & Properties	Description
--prot_modality	string	The name used for the protein modality. Used when input file is a MuData object. When not specified, the protein modality will not be processed.
--prot_raw_layer_input	string	Location of the layer containing the raw protein counts. Layers are looked for in .layers, except when using the value 'X'; in which case .X is used.
--prot_normalized_layer_input	string	Location of the layer containing the normalized counts. Layers are looked for in .layers, except when using the value 'X'; in which case .X is used.

Name

Type & Properties

--prot_modality

string

--prot_raw_layer_input

string

--prot_normalized_layer_input

string

Output slots

Name	Type & Properties	Description
--rna_modality_output	string	TileDB Measurement name where the RNA modality will be stored.
--prot_modality_output	string	Name of the TileDB Measurement where the protein modality will be stored.
--obs_index_name_output	string	Name of the index that is used to describe the cells (observations).
--rna_var_index_name_output	string	Output name of the index that is used to describe the genes.
--rna_raw_layer_output	string	Output location for the raw transcriptomics counts.
--rna_normalized_layer_output	string	Output location for the normalized RNA counts.
--rna_var_gene_names_output	string	Name of the .var column that specifies the gene games.
--prot_var_index_name_output	string	Output name of the index that is used to describe the proteins.
--prot_raw_layer_output	string	Output location for the raw protein counts.
--prot_normalized_layer_output	string	Output location for the normalized protein counts.

Name

Type & Properties

--rna_modality_output

string

--prot_modality_output

string

--obs_index_name_output

string

--rna_var_index_name_output

string

--rna_raw_layer_output

string

--rna_normalized_layer_output

string

--rna_var_gene_names_output

string

--prot_var_index_name_output

string

--prot_raw_layer_output

string

--prot_normalized_layer_output

string

Output arguments

Name	Type & Properties	Description
--tiledb_dir	file output	Directory where the TileDB output will be written to.

Name

Type & Properties

--tiledb_dir

file

output