convert/from_10xh5_to_h5mu

Description

Converts a 10x h5 into an h5mu 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'  
output: "$id.$key.output.h5mu"  
uns_metrics: [ "metrics_cellranger" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	A 10x h5 file as generated by Cell Ranger.
--input_metrics_summary	file	A metrics summary csv file as generated by Cell Ranger.

Name

Type & Properties

--input

-i

file

required

--input_metrics_summary

file

Outputs

Name	Type & Properties	Description
--output -o	file output	Output h5mu file.
--uns_metrics	string	Name of the .uns slot under which to QC metrics (if any).
--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

-o

file

output

--uns_metrics

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--min_genes	integer	Minimum number of counts required for a cell to pass filtering.
--min_counts	integer	Minimum number of genes expressed required for a cell to pass filtering.

Name

Type & Properties

--min_genes

integer

--min_counts

integer