flowchart TB v0(Channel.fromList) v2(filter) v10(filter) v18(totalvi) v25(cross) v35(cross) v41(filter) v50(filter) v65(cross) v75(cross) v84(branch) v111(concat) v96(cross) v106(cross) v115(branch) v142(concat) v127(cross) v137(cross) v146(branch) v173(concat) v158(cross) v168(cross) v180(cross) v190(cross) v196(filter) v350(concat) v205(filter) v220(cross) v230(cross) v239(branch) v266(concat) v251(cross) v261(cross) v270(branch) v297(concat) v282(cross) v292(cross) v301(branch) v328(concat) v313(cross) v323(cross) v335(cross) v345(cross) v357(cross) v364(cross) v376(cross) v383(cross) v387(Output) subgraph group_rna_neighbors_leiden_umap [rna_neighbors_leiden_umap] v58(find_neighbors) v89(leiden) v120(move_obsm_to_obs) v151(umap) end subgraph group_adt_neighbors_leiden_umap [adt_neighbors_leiden_umap] v213(find_neighbors) v244(leiden) v275(move_obsm_to_obs) v306(umap) end v84-->v111 v115-->v142 v146-->v173 v239-->v266 v270-->v297 v301-->v328 v0-->v2 v2-->v10 v10-->v18 v18-->v25 v10-->v25 v10-->v35 v41-->v50 v50-->v58 v58-->v65 v50-->v65 v50-->v75 v84-->v89 v89-->v96 v84-->v96 v84-->v106 v106-->v111 v115-->v120 v120-->v127 v115-->v127 v115-->v137 v137-->v142 v146-->v151 v151-->v158 v146-->v158 v146-->v168 v168-->v173 v173-->v180 v41-->v180 v41-->v190 v196-->v205 v205-->v213 v213-->v220 v205-->v220 v205-->v230 v239-->v244 v244-->v251 v239-->v251 v239-->v261 v261-->v266 v270-->v275 v275-->v282 v270-->v282 v270-->v292 v292-->v297 v301-->v306 v306-->v313 v301-->v313 v301-->v323 v323-->v328 v328-->v335 v196-->v335 v196-->v345 v345-->v350 v350-->v357 v2-->v357 v357-->v364 v2-->v364 v2-->v376 v376-->v383 v2-->v383 v383-->v387 v35-->v41 v18-->v35 v190-->v196 v58-->v75 v75-->v84 v89-->v106 v111-->v115 v120-->v137 v142-->v146 v151-->v168 v173-->v190 v213-->v230 v230-->v239 v244-->v261 v266-->v270 v275-->v292 v297-->v301 v306-->v323 v328-->v345 v350-->v376 style group_rna_neighbors_leiden_umap fill:#F0F0F0,stroke:#969696; style group_adt_neighbors_leiden_umap fill:#F0F0F0,stroke:#969696; style v0 fill:#e3dcea,stroke:#7a4baa; style v2 fill:#e3dcea,stroke:#7a4baa; style v10 fill:#e3dcea,stroke:#7a4baa; style v18 fill:#e3dcea,stroke:#7a4baa; style v25 fill:#e3dcea,stroke:#7a4baa; style v35 fill:#e3dcea,stroke:#7a4baa; style v41 fill:#e3dcea,stroke:#7a4baa; style v50 fill:#e3dcea,stroke:#7a4baa; style v58 fill:#e3dcea,stroke:#7a4baa; style v65 fill:#e3dcea,stroke:#7a4baa; style v75 fill:#e3dcea,stroke:#7a4baa; style v84 fill:#e3dcea,stroke:#7a4baa; style v111 fill:#e3dcea,stroke:#7a4baa; style v89 fill:#e3dcea,stroke:#7a4baa; style v96 fill:#e3dcea,stroke:#7a4baa; style v106 fill:#e3dcea,stroke:#7a4baa; style v115 fill:#e3dcea,stroke:#7a4baa; style v142 fill:#e3dcea,stroke:#7a4baa; style v120 fill:#e3dcea,stroke:#7a4baa; style v127 fill:#e3dcea,stroke:#7a4baa; style v137 fill:#e3dcea,stroke:#7a4baa; style v146 fill:#e3dcea,stroke:#7a4baa; style v173 fill:#e3dcea,stroke:#7a4baa; style v151 fill:#e3dcea,stroke:#7a4baa; style v158 fill:#e3dcea,stroke:#7a4baa; style v168 fill:#e3dcea,stroke:#7a4baa; style v180 fill:#e3dcea,stroke:#7a4baa; style v190 fill:#e3dcea,stroke:#7a4baa; style v196 fill:#e3dcea,stroke:#7a4baa; style v350 fill:#e3dcea,stroke:#7a4baa; style v205 fill:#e3dcea,stroke:#7a4baa; style v213 fill:#e3dcea,stroke:#7a4baa; style v220 fill:#e3dcea,stroke:#7a4baa; style v230 fill:#e3dcea,stroke:#7a4baa; style v239 fill:#e3dcea,stroke:#7a4baa; style v266 fill:#e3dcea,stroke:#7a4baa; style v244 fill:#e3dcea,stroke:#7a4baa; style v251 fill:#e3dcea,stroke:#7a4baa; style v261 fill:#e3dcea,stroke:#7a4baa; style v270 fill:#e3dcea,stroke:#7a4baa; style v297 fill:#e3dcea,stroke:#7a4baa; style v275 fill:#e3dcea,stroke:#7a4baa; style v282 fill:#e3dcea,stroke:#7a4baa; style v292 fill:#e3dcea,stroke:#7a4baa; style v301 fill:#e3dcea,stroke:#7a4baa; style v328 fill:#e3dcea,stroke:#7a4baa; style v306 fill:#e3dcea,stroke:#7a4baa; style v313 fill:#e3dcea,stroke:#7a4baa; style v323 fill:#e3dcea,stroke:#7a4baa; style v335 fill:#e3dcea,stroke:#7a4baa; style v345 fill:#e3dcea,stroke:#7a4baa; style v357 fill:#e3dcea,stroke:#7a4baa; style v364 fill:#e3dcea,stroke:#7a4baa; style v376 fill:#e3dcea,stroke:#7a4baa; style v383 fill:#e3dcea,stroke:#7a4baa; style v387 fill:#e3dcea,stroke:#7a4baa;
Totalvi leiden
Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result.
Info
ID: totalvi_leiden
Namespace: workflows/integration
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 2.1.0 -latest \
-main-script target/nextflow/workflows/integration/totalvi_leiden/main.nf \
--help
Run command
Example of params.yaml
# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"
# layer: "foo"
modality: "rna"
prot_modality: "prot"
reference: # please fill in - example: "path/to/file"
# Outputs
# output: "$id.$key.output.h5mu"
# reference_model_path: "totalvi_model_reference"
# query_model_path: "totalvi_model_query"
# General TotalVI Options
obs_batch: "sample_id"
max_epochs: 400
max_query_epochs: 200
weight_decay: 0.0
force_retrain: false
# var_input: "foo"
# TotalVI integration options RNA
rna_reference_modality: "rna"
rna_obsm_output: "X_totalvi"
# TotalVI integration options ADT
prot_reference_modality: "prot"
prot_obsm_output: "X_totalvi"
# Neighbour calculation RNA
rna_uns_neighbors: "totalvi_integration_neighbors"
rna_obsp_neighbor_distances: "totalvi_integration_distances"
rna_obsp_neighbor_connectivities: "totalvi_integration_connectivities"
# Neighbour calculation ADT
prot_uns_neighbors: "totalvi_integration_neighbors"
prot_obsp_neighbor_distances: "totalvi_integration_distances"
prot_obsp_neighbor_connectivities: "totalvi_integration_connectivities"
# Clustering options RNA
rna_obs_cluster: "totalvi_integration_leiden"
rna_leiden_resolution: [1.0]
# Clustering options ADT
prot_obs_cluster: "totalvi_integration_leiden"
prot_leiden_resolution: [1.0]
# Umap options
obsm_umap: "X_totalvi_umap"
# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
# Arguments
nextflow run openpipelines-bio/openpipeline \
-r 2.1.0 -latest \
-profile docker \
-main-script target/nextflow/workflows/integration/totalvi_leiden/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 |
---|---|---|
--id |
ID of the sample. | string , required, example: "foo" |
--input |
Path to the sample. | file , required, example: "dataset.h5mu" |
--layer |
use specified layer for expression values instead of the .X object from the modality. | string |
--modality |
Which modality to process. | string , default: "rna" |
--prot_modality |
Which modality to process. | string , default: "prot" |
--reference |
Input h5mu file with reference data to train the TOTALVI model. | file , required |
Outputs
Name | Description | Attributes |
---|---|---|
--output |
Destination path to the output. | file , required, example: "output.h5mu" |
--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" |
General TotalVI Options
Name | Description | Attributes |
---|---|---|
--obs_batch |
.Obs column name discriminating between your batches. | string , default: "sample_id" |
--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 |
--force_retrain |
If true, retrain the model and save it to reference_model_path | boolean_true |
--var_input |
Boolean .var column to subset data with (e.g. containing highly variable genes). By default, do not subset genes. | string |
TotalVI integration options RNA
Name | Description | Attributes |
---|---|---|
--rna_reference_modality |
string , default: "rna" |
|
--rna_obsm_output |
In which .obsm slot to store the normalized RNA from TOTALVI. | string , default: "X_totalvi" |
TotalVI integration options ADT
Name | Description | Attributes |
---|---|---|
--prot_reference_modality |
Name of the modality containing proteins in the reference | string , default: "prot" |
--prot_obsm_output |
In which .obsm slot to store the normalized protein data from TOTALVI. | string , default: "X_totalvi" |
Neighbour calculation RNA
Name | Description | Attributes |
---|---|---|
--rna_uns_neighbors |
In which .uns slot to store various neighbor output objects. | string , default: "totalvi_integration_neighbors" |
--rna_obsp_neighbor_distances |
In which .obsp slot to store the distance matrix between the resulting neighbors. | string , default: "totalvi_integration_distances" |
--rna_obsp_neighbor_connectivities |
In which .obsp slot to store the connectivities matrix between the resulting neighbors. | string , default: "totalvi_integration_connectivities" |
Neighbour calculation ADT
Name | Description | Attributes |
---|---|---|
--prot_uns_neighbors |
In which .uns slot to store various neighbor output objects. | string , default: "totalvi_integration_neighbors" |
--prot_obsp_neighbor_distances |
In which .obsp slot to store the distance matrix between the resulting neighbors. | string , default: "totalvi_integration_distances" |
--prot_obsp_neighbor_connectivities |
In which .obsp slot to store the connectivities matrix between the resulting neighbors. | string , default: "totalvi_integration_connectivities" |
Clustering options RNA
Name | Description | Attributes |
---|---|---|
--rna_obs_cluster |
Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for ‘–obs_cluster’ suffixed with an underscore and one of the resolutions resolutions specified in ‘–leiden_resolution’. | string , default: "totalvi_integration_leiden" |
--rna_leiden_resolution |
Control the coarseness of the clustering. Higher values lead to more clusters. | List of double , default: 1 , multiple_sep: ";" |
Clustering options ADT
Name | Description | Attributes |
---|---|---|
--prot_obs_cluster |
Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will be created from the specified value for ‘–obs_cluster’ suffixed with an underscore and one of the resolutions resolutions specified in ‘–leiden_resolution’. | string , default: "totalvi_integration_leiden" |
--prot_leiden_resolution |
Control the coarseness of the clustering. Higher values lead to more clusters. | List of double , default: 1 , multiple_sep: ";" |
Umap options
Name | Description | Attributes |
---|---|---|
--obsm_umap |
In which .obsm slot to store the resulting UMAP embedding. | string , default: "X_totalvi_umap" |