CWL Workflow: SoupX Estimate

Workflow: SoupX Estimate

Fetched 2023-01-09 20:02:38 GMT

Verified with cwltool version 3.1.20221201130942

SoupX Estimate ==============

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.

ID	Type	Title	Doc
fdr	Float (Optional)	FDR cutoff for expression ratio plots	FDR cutoff for expression ratio plots
alias	String	Experiment short name/alias
round_counts	Boolean (Optional)	Round adjusted counts to integers	Round adjusted counts to integers
genelist_file	File [Textual format]	Target genes list. Headerless text file with 1 gene per line	Target genes list. Headerless text file with 1 gene per line
expression_threshold	Float (Optional)	Expression threshold for displaying target genes on a plot (expression > threshold)	Expression threshold for displaying target genes on a plot (expression > threshold)
raw_feature_bc_matrices_folder	File [GZIP format]	scRNA-Seq Cell Ranger Experiment	Compressed folder with unfiltered feature-barcode matrices
secondary_analysis_report_folder	File [GZIP format]	scRNA-Seq Cell Ranger Experiment	Compressed folder with secondary analysis results
filtered_feature_bc_matrix_folder	File [GZIP format]	scRNA-Seq Cell Ranger Experiment	Compressed folder with filtered feature-barcode matrices

ID	Runs	Label	Doc
estimate_contamination	../tools/soupx-subworkflow.cwl (Workflow)	SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination	Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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

Permalink: https://w3id.org/cwl/view/git/9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5/workflows/soupx.cwl