filter/filter_with_pattern

Description

Filter a MuData object based on gene names using a regex.

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"  
var_name_filter: [ "filter_with_pattern" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/filter/filter_with_pattern/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.
--var_gene_names	string	The .var field containing the gene names to be filtered. If not provided, `.var.index` will be used.
--pattern	string required multiple	A regex pattern to filter the gene names.

Name

Type & Properties

--input

file

required

--modality

string

--var_gene_names

string

--pattern

string

required

multiple

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--do_subset	boolean_true	Whether to subset before storing the output.
--var_name_filter	string	In which .var slot to store a boolean array corresponding to which variables 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

--do_subset

boolean_true

--var_name_filter

string

--output_compression

string