filter/do_filter

Description

Remove observations and variables based on specified .obs and .var columns.

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.2 \  
  -main-script target/nextflow/filter/do_filter/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string
--obs_filter	string multiple	Which .obs columns to use to filter the observations by.
--var_filter	string multiple	Which .var columns to use to filter the observations by.
--output	file output	Output h5mu file.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--input

file

required

--modality

string

--obs_filter

string

multiple

--var_filter

string

multiple

--output

file

output

--output_compression

string