wrappers/preprocessing/normalize_total
Description
Normalize counts per cell, running either the GPU (rapids-singlecell) or the
CPU (scanpy) variant of normalize_total, selected with --device_type.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input h5mu file. |
--modality | string | Which modality from the input MuData file to process. |
--input_layer | string | Input layer to use. By default, X is normalized. |
Compute
Name | Type & Properties | Description |
|---|---|---|
--device_type | string | Which implementation to run: the GPU (rapids-singlecell) variant or the CPU (scanpy/squidpy) variant of the component. Selecting `gpu` requires a CUDA-capable GPU; the component errors out if none is available (there is no automatic fallback to CPU). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output h5mu file. |
--output_layer | string | Output layer to use. By default, use X. |
--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 |
|---|---|---|
--target_sum | integer | If not set, after normalization each observation (cell) has a total count equal to the median of total counts for observations (cells) before normalization. |
--exclude_highly_expressed | boolean_true | Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. |
rapids-singlecell options
Name | Type & Properties | Description |
|---|---|---|
--max_fraction | double | If exclude_highly_expressed=True, consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
device_type: [ "gpu" ]
output: "$id.$key.output.h5mu"
max_fraction: [ 0.05 ]
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/wrappers/preprocessing/normalize_total/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
wrappers/preprocessing/normalize_totalopenpipeline_rapids v0.1.3