workflows/ingestion/cellranger_postprocessing
Description
Post-processing Cell Ranger datasets.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--id | string required | ID of the sample. |
--input | file required | Input h5mu file created by running Cell Ranger and converting its output to h5mu. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | The converted h5mu file. |
Correction arguments
Name | Type & Properties | Description |
|---|---|---|
--perform_correction | boolean_true | Whether or not to run CellBender to perform count correction. |
--cellbender_epochs | integer | Number of epochs to run CellBender for. |
Filtering arguments
Name | Type & Properties | Description |
|---|---|---|
--min_genes | integer | Minimum number of counts required for a cell to pass filtering. |
--min_counts | integer | Minimum 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'
id: "run"
output: "$id.$key.output"
cellbender_epochs: [ 150 ]
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/ingestion/cellranger_postprocessingopenpipeline v4.0.0