preprocessing/scrublet
Description
Predict doublets using Scrublet.
Computes a doublet score for each cell from a raw count matrix by simulating
doublets and comparing each observed transcriptome to the simulated ones.
Wraps the rapids-singlecell rsc.pp.scrublet function. Results are written to.obs["doublet_score"], .obs["predicted_doublet"], and .uns["scrublet"].
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 raw counts to run doublet detection on. If not set, `.X` is used. |
--batch_key | string | An optional `.obs` column with batch information. If set, Scrublet is run independently for each batch and the doublet scores are stitched back together. |
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 |
|---|---|---|
--sim_doublet_ratio | double | Number of doublets to simulate relative to the number of observed cells. |
--expected_doublet_rate | double | The estimated doublet rate for the experiment. |
--stdev_doublet_rate | double | Uncertainty in the expected doublet rate. |
--n_prin_comps | integer | Number of principal components used to embed the transcriptomes prior to k-nearest-neighbor graph construction. |
--n_neighbors | integer | Number of neighbors used to construct the KNN graph of observed and simulated transcriptomes. If not set, this is automatically set to round(0.5 * sqrt(n_obs)). |
--threshold | double | Doublet score threshold for calling a transcriptome a doublet. If not set, this is set automatically by looking for the minimum between the two modes of the doublet_scores_sim_ histogram. |
--random_state | integer | Initial state for doublet simulation and nearest neighbors. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output"
sim_doublet_ratio: [ 2 ]
expected_doublet_rate: [ 0.05 ]
stdev_doublet_rate: [ 0.02 ]
n_prin_comps: [ 30 ]
random_state: [ 0 ]
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/scrublet/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
preprocessing/scrubletopenpipeline_rapids v0.1.3
Uses
0 relationships
No component dependencies found.