tiledb/move_mudata_obsm_to_tiledb

Description

Move .obsm items from a MuData modality to an existing tileDB database.
The .obsm keys should not exist in the database yet; and the observations from the modality and
their order should match with what is already present the tiledb database.

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_tiledb: "$id.$key.output_tiledb"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/tiledb/move_mudata_obsm_to_tiledb/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.
--output_modality	string	TileDB-SOMA measurement to add the output to.

Name

Type & Properties

--input_uri

string

required

--s3_region

string

--endpoint

string

--s3_no_sign_request

boolean

--output_modality

string

MuData input

Name	Type & Properties	Description
--input_mudata	file required	MuData object to take the columns from. The observations and their order should match between the database and the input modality.
--modality	string required	Modality where to take the .obsm from.
--obsm_input	string multiple	Keys from .obm to copy. The keys should not be present yet in the database.

Name

Type & Properties

--input_mudata

file

required

--modality

string

required

--obsm_input

string

multiple

TileDB-SOMA output

Name	Type & Properties	Description
--output_tiledb	file output	Output to a directory instead of adding to the existing database.

Name

Type & Properties

--output_tiledb

file

output