workflows/ingestion/conversion

Description

A pipeline to convert different file formats to .h5mu.

Type

nextflow_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 v4.0.2 \  
  -main-script target/nextflow/workflows/ingestion/conversion/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input -i	file required	Path to the sample.
--input_type -t	string required	Type of the input file

Name

Type & Properties

--id

string

required

--input

-i

file

required

--input_type

-t

string

required

Outputs

Name	Type & Properties	Description
--output	file output	Name or template for the output files.

Name

Type & Properties

--output

file

output

Conversion from h5ad

Name	Type & Properties	Description
--modality	string multiple	Name of the modality where the h5ad is stored in the h5mu object.

Name

Type & Properties

--modality

string

multiple