preprocessing/filter_genes
Description
Filter genes based on number of counts or cells.
Keep genes that have at least min_counts counts or are expressed in at least
min_cells cells, or at most max_counts counts or are expressed in at most
max_cells cells. At least one threshold must be provided.
Wraps the rapids-singlecell rsc.pp.filter_genes 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 gene to pass filtering. |
--min_cells | integer | Minimum number of cells expressing a gene required for it to pass filtering. |
--max_counts | integer | Maximum number of counts allowed for a gene to pass filtering. |
--max_cells | integer | Maximum number of cells expressing a gene allowed for it 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_genes/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
preprocessing/filter_genesopenpipeline_rapids v0.1.3
Uses
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