convert/from_tiledb_to_h5mu

Description

No description provided.

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'  
s3_no_sign_request: [ false ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/convert/from_tiledb_to_h5mu/main.nf \  
  -params-file params.yaml

Input database

Name	Type & Properties	Description
--input_uri	string required	A URI pointing to a TileDB-SOMA database.
--s3_region	string	Region where the TileDB-SOMA database is hosted.
--endpoint	string	Custom endpoint to use to connect to S3
--s3_no_sign_request	boolean	Do not sign S3 requests. Credentials will not be loaded if this argument is provided.
--input_modality	string required	TileDB-SOMA measurement to take the input from.
--input_layers	string required multiple	Layers to import from TileDB-SOMA database.

Name

Type & Properties

--input_uri

string

required

--s3_region

string

--endpoint

string

--s3_no_sign_request

boolean

--input_modality

string

required

--input_layers

string

required

multiple

MuData output

Name	Type & Properties	Description
--output	file required output	The output MuData file.
--output_modality	string required	Name of the modality to write the results to.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_modality

string

required

--output_compression

string