ingestion_qc/detect_ingestion_method

Description

Detects the ingestion method of a dataset.
Currently detects either 10X CellRanger Multi, 10X Xenium or Nanostring CosMx, but can be extended to other technologies upon request.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output_uns_ingestion_method: [ "ingestion_method" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_qc.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/ingestion_qc/detect_ingestion_method/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input h5mu file(s)
--modality	string	The modality to use

Name

Type & Properties

--input

file

required

--modality

string

Outputs

Name	Type & Properties	Description
--output_uns_ingestion_method	string	The .uns field in which to store the exprimental setup. Values stored are `cellranger_multi`, `xenium` or `cosmx`.
--output	file required output	The output h5mu file, containing an .uns field with experiment description.

Name

Type & Properties

--output_uns_ingestion_method

string

--output

file

required

output