wrappers/rna/log_normalize
Description
Performs normalization and subsequent log-transformation of raw count data,
running either the GPU (rapids-singlecell) or the CPU (scanpy) variant of the
whole workflow, selected with --device_type.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | MuData file to transform. |
--modality | string | Modality to process. |
--layer | string | Input layer containing raw counts. If not specified, .X is used. |
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). |
Transformation options
Name | Type & Properties | Description |
|---|---|---|
--target_sum | integer | Normalize total counts to the specified amount. If not set, after normalization each observation (cell) will have a total count equal to the median of total counts for observations (cells) before normalization. |
Output slots
Name | Type & Properties | Description |
|---|---|---|
--output_layer | string required | Layer to write the log-transformed counts to. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Destination path to the output. |
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"
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/rna/log_normalize/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
wrappers/rna/log_normalizeopenpipeline_rapids v0.1.3