workflows/ingestion/cellranger_postprocessing

Description

Post-processing Cell Ranger datasets.

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"  
cellbender_epochs: [ 150 ]  
publish_dir: "output/"  
EOM

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

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Input h5mu file created by running Cell Ranger and converting its output to h5mu.

Name

Type & Properties

--id

string

required

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file output	The converted h5mu file.

Name

Type & Properties

--output

file

output

Correction arguments

Name	Type & Properties	Description
--perform_correction	boolean_true	Whether or not to run CellBender to perform count correction.
--cellbender_epochs	integer	Number of epochs to run CellBender for.

Name

Type & Properties

--perform_correction

boolean_true

--cellbender_epochs

integer

Filtering 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