metadata/grep_annotation_column

Description

Perform a regex lookup on a column from the annotation matrices .obs or .var.
The annotation matrix can originate from either a modality, or all modalities (global .var or .obs).

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'  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/metadata/grep_annotation_column/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Path to the input .h5mu.
--input_column	string	Column to query. If not specified, use .var_names or .obs_names, depending on the value of --matrix
--input_layer	string	Input data to use when calculating fraction of observations that match with the query. Only used when --output_fraction_column is provided. If not specified, .X is used.
--modality	string required	Which modality to get the annotation matrix from.
--matrix	string	Matrix to fetch the column from that will be searched.

Name

Type & Properties

--input

-i

file

required

--input_column

string

--input_layer

string

--modality

string

required

--matrix

string

Outputs

Name	Type & Properties	Description
--output -o	file output	Location of the output MuData file.
--output_match_column	string required	Name of the column to write the result to.
--output_fraction_column	string	For the opposite axis, name of the column to write the fraction of observations that matches to the pattern.
--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

-o

file

output

--output_match_column

string

required

--output_fraction_column

string

--output_compression

string

Query options

Name	Type & Properties	Description
--regex_pattern	string required	Regex to use to match with the input column.

Name

Type & Properties

--regex_pattern

string

required