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).
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. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | |
--output_compression | string | The compression format to be used on the output h5mu object. |
--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. |
Query options
Name | Type & Properties | Description |
|---|---|---|
--regex_pattern | string required | Regex to use to match with the input column. |
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 1.0.2 \
-main-script target/nextflow/metadata/grep_annotation_column/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
metadata/grep_annotation_columnopenpipeline 1.0.2
Uses
0 relationships
No component dependencies found.