Totalvi
Performs mapping to the reference by totalvi model: https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scarches_scvi_tools.html#Reference-mapping-with-TOTALVI
Info
ID: totalvi
Namespace: integrate
Links
Example commands
You can run the pipeline using nextflow run
.
View help
You can use --help
as a parameter to get an overview of the possible parameters.
nextflow run openpipelines-bio/openpipeline \
-r 1.0.2 -latest \
-main-script target/nextflow/integrate/totalvi/main.nf \
--help
Run command
Example of params.yaml
# Inputs
input: # please fill in - example: "path/to/file"
reference: # please fill in - example: "path/to/file"
force_retrain: false
query_modality: "rna"
# query_proteins_modality: "foo"
reference_modality: "rna"
reference_proteins_modality: "prot"
# input_layer: "foo"
obs_batch: "sample_id"
# var_input: "foo"
# Outputs
# output: "$id.$key.output.output"
obsm_output: "X_integrated_totalvi"
obsm_normalized_rna_output: "X_totalvi_normalized_rna"
obsm_normalized_protein_output: "X_totalvi_normalized_protein"
# reference_model_path: "$id.$key.reference_model_path.reference_model_path"
# query_model_path: "$id.$key.query_model_path.query_model_path"
# Learning parameters
max_epochs: 400
max_query_epochs: 200
weight_decay: 0.0
# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
-r 1.0.2 -latest \
-profile docker \
-main-script target/nextflow/integrate/totalvi/main.nf \
-params-file params.yaml
Note
Replace -profile docker
with -profile podman
or -profile singularity
depending on the desired backend.
Argument groups
Inputs
Name | Description | Attributes |
---|---|---|
--input |
Input h5mu file with query data to integrate with reference. | file , required |
--reference |
Input h5mu file with reference data to train the TOTALVI model. | file , required |
--force_retrain |
If true, retrain the model and save it to reference_model_path | boolean_true |
--query_modality |
string , default: "rna" |
|
--query_proteins_modality |
Name of the modality in the input (query) h5mu file containing protein data | string |
--reference_modality |
string , default: "rna" |
|
--reference_proteins_modality |
Name of the modality containing proteins in the reference | string , default: "prot" |
--input_layer |
Input layer to use. If None, X is used | string |
--obs_batch |
Column name discriminating between your batches. | string , default: "sample_id" |
--var_input |
.var column containing highly variable genes. By default, do not subset genes. | string |
Outputs
Name | Description | Attributes |
---|---|---|
--output |
Output h5mu file. | file , required |
--obsm_output |
In which .obsm slot to store the resulting integrated embedding. | string , default: "X_integrated_totalvi" |
--obsm_normalized_rna_output |
In which .obsm slot to store the normalized RNA from TOTALVI. | string , default: "X_totalvi_normalized_rna" |
--obsm_normalized_protein_output |
In which .obsm slot to store the normalized protein data from TOTALVI. | string , default: "X_totalvi_normalized_protein" |
--reference_model_path |
Directory with the reference model. If not exists, trained model will be saved there | file , default: "totalvi_model_reference" |
--query_model_path |
Directory, where the query model will be saved | file , default: "totalvi_model_query" |
Learning parameters
Name | Description | Attributes |
---|---|---|
--max_epochs |
Number of passes through the dataset | integer , default: 400 |
--max_query_epochs |
Number of passes through the dataset, when fine-tuning model for query | integer , default: 200 |
--weight_decay |
Weight decay, when fine-tuning model for query | double , default: 0 |