workflows/gdo/gdo_singlesample

Description

Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.

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 v3.0.2 \  
  -main-script target/nextflow/workflows/gdo/gdo_singlesample/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Path to the sample.
--layer	string	Input layer to start from. By default, .X will be used.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

Output

Name	Type & Properties	Description
--output	file required output	Destination path to the output.

Name

Type & Properties

--output

file

required

output

Filtering options

Name	Type & Properties	Description
--min_counts	integer	Minimum number of counts captured per cell.
--max_counts	integer	Maximum number of counts captured per cell.
--min_guides_per_cell	integer	Minimum of non-zero values per cell.
--max_guides_per_cell	integer	Maximum of non-zero values per cell.
--min_cells_per_guide	integer	Minimum of non-zero values per gene.

Name

Type & Properties

--min_counts

integer

--max_counts

integer

--min_guides_per_cell

integer

--max_guides_per_cell

integer

--min_cells_per_guide

integer