workflows/multiomics/process_singlesample

Description

A pipeline to analyse a single multiomics sample.

Type

nextflow_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.h5mu"  
add_id_to_obs: [ true ]  
add_id_obs_output: [ "sample_id" ]  
add_id_make_observation_keys_unique: [ true ]  
mitochondrial_gene_regex: [ "^[mM][tT]-" ]  
ribosomal_gene_regex: [ "^[Mm]?[Rr][Pp][LlSs]" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/workflows/multiomics/process_singlesample/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--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

--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.
--rna_min_fraction_ribo	double	Minimum fraction of UMIs that are mitochondrial.
--rna_max_fraction_ribo	double	Maximum fraction of UMIs that are mitochondrial.
--skip_scrublet_doublet_detection	boolean_true	Skip the scrublet doublet detection step.
--scrublet_score_threshold	double	Manual doublet score threshold passed to filter_with_scrublet. Cells with a doublet score above this value are classified as doublets. If not provided, the threshold is determined automatically by Scrublet.

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

--rna_min_fraction_ribo

double

--rna_max_fraction_ribo

double

--skip_scrublet_doublet_detection

boolean_true

--scrublet_score_threshold

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

Cross-modality filtering

Name	Type & Properties	Description
--intersect_obs	boolean_true	After per-modality filtering, remove observations that are not present in all processed modalities so that each modality shares the same set of cells.

Name

Type & Properties

--intersect_obs

boolean_true

Mitochondrial & Ribosomal Gene Detection

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

Name

Type & Properties

--var_gene_names

string

--var_name_mitochondrial_genes

string

--obs_name_mitochondrial_fraction

string

--mitochondrial_gene_regex

string

--var_name_ribosomal_genes

string

--obs_name_ribosomal_fraction

string

--ribosomal_gene_regex

string