convert/from_bdrhap_to_h5mu

Description

Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.

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'  
id: "run"  
output: "$id.$key.output.h5mu"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/convert/from_bdrhap_to_h5mu/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

Inputs

Name	Type & Properties	Description
--id	string required	A sample ID.
--input -i	file required	The output h5mu of a BD Rhapsody workflow.

Name

Type & Properties

--id

string

required

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.

Name

Type & Properties

--output

-o

file

required

output