workflows/rna/rna_singlesample

Description

Processing unimodal single-sample RNA transcriptomics data.

Input

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required	Path to the sample.
--layer	string	Input layer to start from. By default, .X will be used.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

Output

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

Name

Type & Properties

--output

file

required

output

Filtering options

Name	Type & Properties	Description
--min_counts	integer	Minimum number of counts captured per cell.
--max_counts	integer	Maximum number of counts captured per cell.
--min_genes_per_cell	integer	Minimum of non-zero values per cell.
--max_genes_per_cell	integer	Maximum of non-zero values per cell.
--min_cells_per_gene	integer	Minimum of non-zero values per gene.
--min_fraction_mito	double	Minimum fraction of UMIs that are mitochondrial. Requires --obs_name_mitochondrial_fraction.
--max_fraction_mito	double	Maximum fraction of UMIs that are mitochondrial. Requires --obs_name_mitochondrial_fraction.
--min_fraction_ribo	double	Minimum fraction of UMIs that are ribosomal. Requires --obs_name_ribosomal_fraction.
--max_fraction_ribo	double	Maximum fraction of UMIs that are ribosomal. Requires --obs_name_ribosomal_fraction.
--skip_scrublet_doublet_detection	boolean_true	Skip the scrublet doublet detection step.

Name

Type & Properties

--min_counts

integer

--max_counts

integer

--min_genes_per_cell

integer

--max_genes_per_cell

integer

--min_cells_per_gene

integer

--min_fraction_mito

double

--max_fraction_mito

double

--min_fraction_ribo

double

--max_fraction_ribo

double

--skip_scrublet_doublet_detection

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

Run this component

Run the following command to execute this component with Nextflow:

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

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

workflows/rna/rna_singlesample

Input

Output

Filtering options

Mitochondrial & Ribosomal Gene Detection

Run this component

Relationships

Used by

Uses