wrappers/preprocessing/log1p
Description
Logarithmize the data matrix, running either the GPU (rapids-singlecell) or
the CPU (scanpy) variant of log1p, selected with --device_type.
Computes X = log(X + 1), where log denotes the natural logarithm unless
a different base is given.
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. If not set, .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). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output h5mu file. |
--output_layer | string | Output layer to write the transformed matrix to. If not set: when --input_layer is unset, .X is modified in-place; when --input_layer is set, that input layer is modified in-place. |
--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 |
|---|---|---|
--base | double | Base of the logarithm. If unset, the natural logarithm is used. |
rapids-singlecell options
Name | Type & Properties | Description |
|---|---|---|
--input_obsm | string | Entry in .obsm to log-transform. Mutually exclusive with --input_layer. |
--output_obsm | string | Output entry in .obsm to write the transformed matrix to. Only valid when --input_obsm is set. If not set, the input .obsm entry is modified in-place. Mutually exclusive with --output_layer. |
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/preprocessing/log1p/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
wrappers/preprocessing/log1popenpipeline_rapids v0.1.3