filter/subset_obsp

Description

Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot.

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.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.1 \  
  -main-script target/nextflow/filter/subset_obsp/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--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_compression

string

Input

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--input_obsp_key	string required	The .obsp field to be filtered.
--input_obs_key	string required	The .obs column to filter on.
--input_obs_value	string required	The value to filter on in the .obs column.

Name

Type & Properties

--input

file

required

--modality

string

--input_obsp_key

string

required

--input_obs_key

string

required

--input_obs_value

string

required

Output

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--output_obsm_key	string required	The .obsm key to store the subset in.

Name

Type & Properties

--output

file

output

--output_obsm_key

string

required