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.

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'  
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

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.

Name

Type & Properties

--input

file

required

--modality

string

--obs_feature

string

required

--drop_obs_nan

boolean_true

--ensure_unique_filenames

boolean_true

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.

Name

Type & Properties

--output

file

required

output

--output_files

file

required

output

--output_compression

string