workflows/multiomics/process_samples

Description

A pipeline to analyse multiple multiomics samples.

Type

nextflow_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
output: "$id.$key.output.h5mu"  
add_id_to_obs: [ true ]  
add_id_obs_output: [ "sample_id" ]  
add_id_make_observation_keys_unique: [ true ]  
highly_variable_features_var_output: [ "filter_with_hvg" ]  
highly_variable_features_obs_batch_key: [ "sample_id" ]  
mitochondrial_gene_regex: [ "^[mM][tT]-" ]  
top_n_vars: [ 50, 100, 200, 500 ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/workflows/multiomics/process_samples/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input -i	file required	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.
--gdo_layer	string	Input layer for the guide-derived oligonucleotide (GDO) data. If not specified, .X is used.

Name

Type & Properties

--id

string

required

--input

-i

file

required

--rna_layer

string

--prot_layer

string

--gdo_layer

string

Outputs

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

Name

Type & Properties

--output

file

required

output

Sample ID options

Name	Type & Properties	Description
--add_id_to_obs	boolean	Add the value passed with --id to .obs.
--add_id_obs_output	string	.Obs column to add the sample IDs to. Required and only used when --add_id_to_obs is set to 'true'
--add_id_make_observation_keys_unique	boolean	Join the id to the .obs index (.obs_names). Only used when --add_id_to_obs is set to 'true'.

Name

Type & Properties

--add_id_to_obs

boolean

--add_id_obs_output

string

--add_id_make_observation_keys_unique

boolean

RNA filtering options

Name	Type & Properties	Description
--rna_min_counts	integer	Minimum number of counts captured per cell.
--rna_max_counts	integer	Maximum number of counts captured per cell.
--rna_min_genes_per_cell	integer	Minimum of non-zero values per cell.
--rna_max_genes_per_cell	integer	Maximum of non-zero values per cell.
--rna_min_cells_per_gene	integer	Minimum of non-zero values per gene.
--rna_min_fraction_mito	double	Minimum fraction of UMIs that are mitochondrial.
--rna_max_fraction_mito	double	Maximum fraction of UMIs that are mitochondrial.

Name

Type & Properties

--rna_min_counts

integer

--rna_max_counts

integer

--rna_min_genes_per_cell

integer

--rna_max_genes_per_cell

integer

--rna_min_cells_per_gene

integer

--rna_min_fraction_mito

double

--rna_max_fraction_mito

double

CITE-seq filtering options

Name	Type & Properties	Description
--prot_min_counts	integer	Minimum number of counts per cell.
--prot_max_counts	integer	Minimum number of counts per cell.
--prot_min_proteins_per_cell	integer	Minimum of non-zero values per cell.
--prot_max_proteins_per_cell	integer	Maximum of non-zero values per cell.
--prot_min_cells_per_protein	integer	Minimum of non-zero values per protein.

Name

Type & Properties

--prot_min_counts

integer

--prot_max_counts

integer

--prot_min_proteins_per_cell

integer

--prot_max_proteins_per_cell

integer

--prot_min_cells_per_protein

integer

GDO filtering options

Name	Type & Properties	Description
--gdo_min_counts	integer	Minimum number of counts per cell.
--gdo_max_counts	integer	Minimum number of counts per cell.
--gdo_min_guides_per_cell	integer	Minimum of non-zero values per cell.
--gdo_max_guides_per_cell	integer	Maximum of non-zero values per cell.
--gdo_min_cells_per_guide	integer	Minimum of non-zero values per guide.

Name

Type & Properties

--gdo_min_counts

integer

--gdo_max_counts

integer

--gdo_min_guides_per_cell

integer

--gdo_max_guides_per_cell

integer

--gdo_min_cells_per_guide

integer

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

Mitochondrial Gene Detection

Name	Type & Properties	Description
--var_name_mitochondrial_genes	string	In which .var slot to store a boolean array corresponding the mitochondrial genes.
--obs_name_mitochondrial_fraction	string	When specified, write the fraction of counts originating from mitochondrial genes (based on --mitochondrial_gene_regex) to an .obs column with the specified name. Requires --var_name_mitochondrial_genes.
--var_gene_names	string	.var column name to be used to detect mitochondrial genes instead of .var_names (default if not set). Gene names matching with the regex value from --mitochondrial_gene_regex will be identified as a mitochondrial gene.
--mitochondrial_gene_regex	string	Regex string that identifies mitochondrial genes from --var_gene_names. By default will detect human and mouse mitochondrial genes from a gene symbol.

Name

Type & Properties

--var_name_mitochondrial_genes

string

--obs_name_mitochondrial_fraction

string

--var_gene_names

string

--mitochondrial_gene_regex

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. Defaults to the combined values specified for --var_name_mitochondrial_genes and --highly_variable_features_var_output.
--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