integrate/scarches

Description

Performs reference mapping with scArches

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file to use as a query
--layer	string	Layer to be used for scArches, if .X is not to be used.
--modality	string	Which modality from the input MuData file to process.
--input_obs_batch	string	Name of the .obs column with batch information.
--input_obs_label	string	Name of the .obs column with celltype information.
--input_var_gene_names	string	Name of the .var column with gene names, if the var .index is not to be used.
--input_obs_size_factor	string	Key in adata.obs for size factor information. Instead of using library size as a size factor, the provided size factor column will be used as offset in the mean of the likelihood. Assumed to be on linear scale.

Name

Type & Properties

--input

-i

file

required

--layer

string

--modality

string

--input_obs_batch

string

--input_obs_label

string

--input_var_gene_names

string

--input_obs_size_factor

string

Reference

Name	Type & Properties	Description
--reference -r	file required	Path to the directory with reference model or a web link.
--reference_class	string	For legacy models; the type of model (where the type of model was not saved with it; e.g. when they were generated with scvi-tools versions < 0.15).

Name

Type & Properties

--reference

-r

file

required

--reference_class

string

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--model_output	file output	Output directory for model
--obsm_output	string	In which .obsm slot to store the resulting integrated embedding.
--obs_output_predictions	string	In which .obs slot to store the resulting label predictions. Only relevant if a scANVI model was provided.
--obs_output_probabilities	string	In which .obs slot to store the probabilities of the label predictions. Only relevant if a scANVI model was provided.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

-o

file

required

output

--model_output

file

output

--obsm_output

string

--obs_output_predictions

string

--obs_output_probabilities

string

--output_compression

string

Early stopping arguments

Name	Type & Properties	Description
--early_stopping	boolean	Whether to perform early stopping with respect to the validation set.
--early_stopping_monitor	string	Metric logged during validation set epoch.
--early_stopping_patience	integer	Number of validation epochs with no improvement after which training will be stopped.
--early_stopping_min_delta	double	Minimum change in the monitored quantity to qualify as an improvement, i.e. an absolute change of less than min_delta, will count as no improvement.

Name

Type & Properties

--early_stopping

boolean

--early_stopping_monitor

string

--early_stopping_patience

integer

--early_stopping_min_delta

double

Learning parameters

Name	Type & Properties	Description
--max_epochs	integer	Number of passes through the dataset, defaults to (20000 / number of cells) * 400 or 400; whichever is smallest.
--reduce_lr_on_plateau	boolean	Whether to monitor validation loss and reduce learning rate when validation set `lr_scheduler_metric` plateaus.
--lr_factor	double	Factor to reduce learning rate.
--lr_patience	double	Number of epochs with no improvement after which learning rate will be reduced.

Name

Type & Properties

--max_epochs

integer

--reduce_lr_on_plateau

boolean

--lr_factor

double

--lr_patience

double

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output"  
model_output: "$id.$key.model_output"  
obsm_output: [ "X_integrated_scanvi" ]  
obs_output_predictions: [ "scanvi_pred" ]  
obs_output_probabilities: [ "scanvi_proba" ]  
early_stopping_monitor: [ "elbo_validation" ]  
early_stopping_patience: [ 45 ]  
early_stopping_min_delta: [ 0 ]  
reduce_lr_on_plateau: [ true ]  
lr_factor: [ 0.6 ]  
lr_patience: [ 30 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/integrate/scarches/main.nf \  
  -params-file params.yaml

integrate/scarches

Inputs

Reference

Outputs

Early stopping arguments

Learning parameters

Run this component

Relationships

Used by

Uses