convert/velocyto_to_h5mu

Description

Convert a velocyto loom file to a h5mu file.

If an input h5mu file is also provided, the velocity
h5ad object will get added to that h5mu instead.

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_velocity" ]  
output: "$id.$key.output.h5mu"  
layer_spliced: [ "velo_spliced" ]  
layer_unspliced: [ "velo_unspliced" ]  
layer_ambiguous: [ "velo_ambiguous" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_loom	file required	Path to the input loom file.
--input_h5mu	file	If a MuData file is provided,
--modality	string	The name of the modality to operate on.

Name

Type & Properties

--input_loom

file

required

--input_h5mu

file

--modality

string

Outputs

Name	Type & Properties	Description
--output	file output	Path to the output MuData file.
--layer_spliced	string	Output layer for the spliced reads.
--layer_unspliced	string	Output layer for the unspliced reads.
--layer_ambiguous	string	Output layer for the ambiguous reads.
--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

output

--layer_spliced

string

--layer_unspliced

string

--layer_ambiguous

string

--output_compression

string