preprocessing/filter_cells
Description
Filter cell outliers based on counts and numbers of genes expressed.
Keep cells that have at least min_counts counts or min_genes genes expressed,
and at most max_counts counts or max_genes genes expressed. The thresholds
are applied to the counts in X on the GPU and the AnnData is subsetted in
place. Wraps the rapids-singlecell rsc.pp.filter_cells function.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input h5mu file. |
--modality | string | Which modality from the input MuData file to process. |
--layer | string | Layer of counts to filter on. If not set, .X is used. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output h5mu file. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Options
Name | Type & Properties | Description |
|---|---|---|
--min_counts | integer | Minimum number of counts required for a cell to pass filtering. |
--min_genes | integer | Minimum number of genes expressed required for a cell to pass filtering. |
--max_counts | integer | Maximum number of counts required for a cell to pass filtering. |
--max_genes | integer | Maximum number of genes expressed required for a cell to pass filtering. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_rapids.git \
-revision v0.1.3 \
-main-script target/nextflow/preprocessing/filter_cells/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
preprocessing/filter_cellsopenpipeline_rapids v0.1.3
Uses
0 relationships
No component dependencies found.