workflows/qc/spatial_qc

Description

A pipeline to add basic qc statistics to a MuData containing spatial data.

Type

nextflow_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
modality: [ "rna" ]  
mitochondrial_gene_regex: [ "^[mM][tT]-" ]  
ribosomal_gene_regex: [ "^[Mm]?[Rr][Pp][LlSs]" ]  
top_n_vars: [ 50, 100, 200, 500 ]  
output_obs_num_nonzero_vars: [ "num_nonzero_vars" ]  
output_obs_total_counts_vars: [ "total_counts" ]  
output_var_num_nonzero_obs: [ "num_nonzero_obs" ]  
output_var_total_counts_obs: [ "total_counts" ]  
output_var_obs_mean: [ "obs_mean" ]  
output_var_pct_dropout: [ "pct_dropout" ]  
output: "$id.$key.output.h5mu"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/workflows/qc/spatial_qc/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.
--modality	string	Which modality to process.
--layer	string	Use specified layer for calculation of qc metrics. If not specified, adata.X is used.

Name

Type & Properties

--id

string

required

--input

-i

file

required

--modality

string

--layer

string

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	.Obs slot to store the fraction of reads found to be mitochondrial. Defaults to 'fraction_' suffixed by the value of --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

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 value from --var_name_mitochondrial_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.
--output_obs_num_nonzero_vars	string	Name of column in .obs describing, for each observation, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each row the number of columns that contain data.
--output_obs_total_counts_vars	string	Name of the column for .obs describing, for each observation (row), the sum of the stored values in the columns.
--output_var_num_nonzero_obs	string	Name of column describing, for each feature, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each column the number of rows that contain data.
--output_var_total_counts_obs	string	Name of the column in .var describing, for each feature (column), the sum of the stored values in the rows.
--output_var_obs_mean	string	Name of the column in .obs providing the mean of the values in each row.
--output_var_pct_dropout	string	Name of the column in .obs providing for each feature the percentage of observations the feature does not appear on (i.e. is missing). Same as `--output_var_num_nonzero_obs` but percentage based.

Name

Type & Properties

--var_qc_metrics

string

multiple

--top_n_vars

integer

multiple

--output_obs_num_nonzero_vars

string

--output_obs_total_counts_vars

string

--output_var_num_nonzero_obs

string

--output_var_total_counts_obs

string

--output_var_obs_mean

string

--output_var_pct_dropout

string

Outputs

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

Name

Type & Properties

--output

file

required

output