tiledb/move_mudata_obs_to_tiledb
Description
Move .obs columns from a MuData modality to an existing tileDB database.
The .obs 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.
Input database
Name | Type & Properties | Description |
|---|---|---|
--input_uri | string | A URI pointing to a TileDB-SOMA database. Mutually exclusive with 'input_dir' |
--input_dir | file | Path to a TileDB-SOMA database as a local directory |
--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. |
--obs_index_name_input | string | Name of the index that is used to describe the cells (observations). |
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 .obs from. |
--obs_input | string multiple | Columns from .obs to copy. The keys should not be present yet in the database. |
TileDB-SOMA output
Name | Type & Properties | Description |
|---|---|---|
--output_tiledb | file output | Output to a directory instead of adding to the existing database. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
s3_no_sign_request: [ false ]
obs_index_name_input: [ "cell_id" ]
output_tiledb: "$id.$key.output_tiledb"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf \
-params-file params.yaml Relationships
Used by
2 relationships
Current component
tiledb/move_mudata_obs_to_tiledbopenpipeline v4.0.0
Uses
0 relationships
No component dependencies found.