dataflow/split_h5mu
Description
Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality.
Input & specifications
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Path to a single .h5mu file. |
--modality | string | Which modality from the input MuData file to process. |
--obs_feature | string required | The .obs column to split the mudata on. |
--drop_obs_nan | boolean_true | Whether to drop all .obs columns that contain only nan values after splitting. |
--ensure_unique_filenames | boolean_true | Append number suffixes to ensure unique filenames after sanitizing obs feature values. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output directory containing multiple h5mu files. |
--output_files | file required output | A csv containing the base filename and obs feature by which it was split. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output./path/to/output"
output_files: "$id.$key.output_files.csv"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/dataflow/split_h5mu/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
dataflow/split_h5muopenpipeline v4.0.0
Uses
0 relationships
No component dependencies found.