filter/delimit_fraction

Description

Turns a column containing values between 0 and 1 into a boolean column based on thresholds.

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" ]  
output: "$id.$key.output.h5mu"  
min_fraction: [ 0 ]  
max_fraction: [ 1 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.1 \  
  -main-script target/nextflow/filter/delimit_fraction/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--obs_fraction_column	string required	Name of column from .var dataframe selecting a column that contains floating point values between 0 and 1.

Name

Type & Properties

--input

file

required

--modality

string

--obs_fraction_column

string

required

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--obs_name_filter	string required	In which .obs slot to store a boolean array corresponding to which observations should be removed.
--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

--obs_name_filter

string

required

--output_compression

string

Arguments

Name	Type & Properties	Description
--min_fraction	double	Min fraction for an observation to be retained (True in output).
--max_fraction	double	Max fraction for an observation to be retained (True in output).

Name

Type & Properties

--min_fraction

double

--max_fraction

double