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.

Type

nextflow_script

Contributors

Launch

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 ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.4 \  
  -main-script target/nextflow/workflows/multiomics/process_batches/main.nf \  
  -params-file params.yaml

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