SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Workflow: SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Fetched 2025-03-08 03:59:53 GMT

Verified with cwltool version 3.1.20230201224320

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Doc
fdr	Float (Optional)	FDR cutoff for expression ratio plots
round_counts	Boolean (Optional)	Round adjusted counts to integers
genelist_file	File (Optional)	Target genes list. Headerless text file with 1 gene per line
output_prefix	String (Optional)	Output prefix
expression_threshold	Float (Optional)	Expression threshold for displaying target genes on a plot (expression > threshold)
matrix_format_version	https://w3id.org/cwl/view/git/7826a52718f052b53cc3872dcb3619a61babb44b/tools/soupx-subworkflow.cwl#matrix_format_version/matrix_format_version (Optional)	Output matrix format version. Corresponds to the latest Cell Ranger matrix format
raw_feature_bc_matrices_folder	File	Compressed folder with unfiltered feature-barcode matrices
secondary_analysis_report_folder	File	Compressed folder with secondary analysis results
filtered_feature_bc_matrix_folder	File	Compressed folder with filtered feature-barcode matrices

Steps

ID	Runs	Label	Doc
estimate_contamination	soupx.cwl (CommandLineTool)	SoupX - an R package for the estimation and removal of cell free mRNA contamination	In droplet based, single cell RNA-seq experiments, there is always a certain amount of background mRNAs present in the dilution that gets distributed into the droplets with cells and sequenced along with them. The net effect of this is to produce a background contamination that represents expression not from the cell contained within a droplet, but the solution that contained the cells. This collection of cell free mRNAs floating in the input solution (henceforth referred to as “the soup”) is created from cells in the input solution being lysed. Because of this, the soup looks different for each input solution and strongly resembles the expression pattern obtained by summing all the individual cells. The aim of this package is to provide a way to estimate the composition of this soup, what fraction of UMIs are derived from the soup in each droplet and produce a corrected count table with the soup based expression removed. The method to do this consists of three parts: - Calculate the profile of the soup. - Estimate the cell specific contamination fraction. - Infer a corrected expression matrix.
extract_count_matrices_to_folder	soupx-subworkflow.cwl#extract_count_matrices_to_folder/1d1d6eb7-f1d5-43d4-bdfa-83c135376277 (CommandLineTool)
compress_adjusted_feature_bc_matrices_folder	tar-compress.cwl (CommandLineTool)	TAR compress	TAR compress ========================================= Creates compressed TAR file from a folder

Outputs

ID	Type	Doc
soupx_stderr_log	File	SoupX stderr log
soupx_stdout_log	File	SoupX stdout log
raw_gene_expression_plots	File (Optional)	Raw gene expression plots
contamination_estimation_plot	File	Contamination estimation plot
adjusted_gene_expression_plots	File (Optional)	Adjusted gene expression plots
adjusted_feature_bc_matrices_h5	File	Adjusted feature-barcode matrices in HDF5 format
adjusted_feature_bc_matrices_folder	File	Compressed folder with adjusted feature-barcode matrices in MEX format
raw_to_adjusted_gene_expression_ratio_plots	File (Optional)	Raw to adjusted gene expression ratio plots
raw_gene_expression_to_pure_soup_ratio_plots	File (Optional)	Raw gene expression to pure soup ratio plots

Permalink: https://w3id.org/cwl/view/git/7826a52718f052b53cc3872dcb3619a61babb44b/tools/soupx-subworkflow.cwl