- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
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 |
Steps
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. |
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 |
https://w3id.org/cwl/view/git/9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5/workflows/soupx.cwl