workflows/multiomics/process_batches

Description

This workflow serves as an entrypoint into the 'full_pipeline' in order to
re-run the multisample processing and the integration setup. An input .h5mu file will
first be split in order to run the multisample processing per modality. Next, the modalities
are merged again and the integration setup pipeline is executed. Please note that this workflow
assumes that samples from multiple pipelines are already concatenated.

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input -i	file required multiple	Path to the sample.
--rna_layer	string	Input layer for the gene expression modality. If not specified, .X is used.
--prot_layer	string	Input layer for the antibody capture modality. If not specified, .X is used.

Name

Type & Properties

--id

string

required

--input

-i

file

required

multiple

--rna_layer

string

--prot_layer

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.

Name

Type & Properties

--output

file

required

output

Highly variable features detection

Name	Type & Properties	Description
--highly_variable_features_var_output --filter_with_hvg_var_output	string	In which .var slot to store a boolean array corresponding to the highly variable genes.
--highly_variable_features_obs_batch_key --filter_with_hvg_obs_batch_key	string	If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method.

Name

Type & Properties

--highly_variable_features_var_output

--filter_with_hvg_var_output

string

--highly_variable_features_obs_batch_key

--filter_with_hvg_obs_batch_key

string

QC metrics calculation options

Name	Type & Properties	Description
--var_qc_metrics	string multiple	Keys to select a boolean (containing only True or False) column from .var. For each cell, calculate the proportion of total values for genes which are labeled 'True', compared to the total sum of the values for all genes.
--top_n_vars	integer multiple	Number of top vars to be used to calculate cumulative proportions. If not specified, proportions are not calculated. `--top_n_vars 20,50` finds cumulative proportion to the 20th and 50th most expressed vars.

Name

Type & Properties

--var_qc_metrics

string

multiple

--top_n_vars

integer

multiple

PCA options

Name	Type & Properties	Description
--pca_overwrite	boolean_true	Allow overwriting slots for PCA output.

Name

Type & Properties

--pca_overwrite

boolean_true

CLR options

Name	Type & Properties	Description
--clr_axis	integer	Axis to perform the CLR transformation on.

Name

Type & Properties

--clr_axis

integer

RNA Scaling options

Name	Type & Properties	Description
--rna_enable_scaling	boolean_true	Enable scaling for the RNA modality.
--rna_scaling_output_layer	string	Output layer where the scaled log-normalized data will be stored.
--rna_scaling_pca_obsm_output	string	Name of the .obsm key where the PCA representation of the log-normalized and scaled data is stored.
--rna_scaling_pca_loadings_varm_output	string	Name of the .varm key where the PCA loadings of the log-normalized and scaled data is stored.
--rna_scaling_pca_variance_uns_output	string	Name of the .uns key where the variance and variance ratio will be stored as a map. The map will contain two keys: variance and variance_ratio respectively.
--rna_scaling_umap_obsm_output	string	Name of the .obsm key where the UMAP representation of the log-normalized and scaled data is stored.
--rna_scaling_max_value	double	Clip (truncate) data to this value after scaling. If not specified, do not clip.
--rna_scaling_zero_center	boolean_false	If set, omit zero-centering variables, which allows to handle sparse input efficiently."

Name

Type & Properties

--rna_enable_scaling

boolean_true

--rna_scaling_output_layer

string

--rna_scaling_pca_obsm_output

string

--rna_scaling_pca_loadings_varm_output

string

--rna_scaling_pca_variance_uns_output

string

--rna_scaling_umap_obsm_output

string

--rna_scaling_max_value

double

--rna_scaling_zero_center

boolean_false

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
output: "$id.$key.output.h5mu"  
highly_variable_features_var_output: [ "filter_with_hvg" ]  
highly_variable_features_obs_batch_key: [ "sample_id" ]  
var_qc_metrics: [ "filter_with_hvg" ]  
top_n_vars: [ 50, 100, 200, 500 ]  
clr_axis: [ 0 ]  
rna_scaling_output_layer: [ "scaled" ]  
rna_scaling_pca_obsm_output: [ "scaled_pca" ]  
rna_scaling_pca_loadings_varm_output: [ "scaled_pca_loadings" ]  
rna_scaling_pca_variance_uns_output: [ "scaled_pca_variance" ]  
rna_scaling_umap_obsm_output: [ "scaled_umap" ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/workflows/multiomics/process_batches/main.nf \  
  -params-file params.yaml

workflows/multiomics/process_batches

Inputs

Outputs

Highly variable features detection

QC metrics calculation options

PCA options

CLR options

RNA Scaling options

Run this component

Relationships

Used by

Uses