cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement 'sd:upstream': sc_rnaseq_sample: - "single-cell-preprocess-cellranger.cwl" - "cellranger-aggr.cwl" inputs: alias: type: string label: "Experiment short name/alias" sd:preview: position: 1 raw_feature_bc_matrices_folder: type: File format: "http://edamontology.org/format_3989" label: "scRNA-Seq Cell Ranger Experiment" doc: "Compressed folder with unfiltered feature-barcode matrices" 'sd:upstreamSource': "sc_rnaseq_sample/raw_feature_bc_matrices_folder" 'sd:localLabel': true filtered_feature_bc_matrix_folder: type: File format: "http://edamontology.org/format_3989" label: "scRNA-Seq Cell Ranger Experiment" doc: "Compressed folder with filtered feature-barcode matrices" 'sd:upstreamSource': "sc_rnaseq_sample/filtered_feature_bc_matrix_folder" 'sd:localLabel': true secondary_analysis_report_folder: type: File format: "http://edamontology.org/format_3989" label: "scRNA-Seq Cell Ranger Experiment" doc: "Compressed folder with secondary analysis results" 'sd:upstreamSource': "sc_rnaseq_sample/secondary_analysis_report_folder" 'sd:localLabel': true genelist_file: type: File format: "http://edamontology.org/format_2330" label: "Target genes list. Headerless text file with 1 gene per line" doc: "Target genes list. Headerless text file with 1 gene per line" expression_threshold: type: float? default: 0 label: "Expression threshold for displaying target genes on a plot (expression > threshold)" doc: "Expression threshold for displaying target genes on a plot (expression > threshold)" 'sd:layout': advanced: true fdr: type: float? default: 0.05 label: "FDR cutoff for expression ratio plots" doc: "FDR cutoff for expression ratio plots" 'sd:layout': advanced: true round_counts: type: boolean? default: false label: "Round adjusted counts to integers" doc: "Round adjusted counts to integers" 'sd:layout': advanced: true outputs: adjusted_feature_bc_matrices_folder: type: File format: "http://edamontology.org/format_3989" outputSource: estimate_contamination/adjusted_feature_bc_matrices_folder label: "Compressed folder with adjusted feature-barcode matrices in MEX format" doc: "Compressed folder with adjusted feature-barcode matrices in MEX format" adjusted_feature_bc_matrices_h5: type: File format: "http://edamontology.org/format_3590" outputSource: estimate_contamination/adjusted_feature_bc_matrices_h5 label: "Adjusted feature-barcode matrices in HDF5 format" doc: "Adjusted feature-barcode matrices in HDF5 format" contamination_estimation_plot: type: File format: "http://edamontology.org/format_3508" outputSource: estimate_contamination/contamination_estimation_plot label: "Contamination estimation plot" doc: "Contamination estimation plot" raw_gene_expression_plots: type: File? format: "http://edamontology.org/format_3508" outputSource: estimate_contamination/raw_gene_expression_plots label: "Raw gene expression plots" doc: "Raw gene expression plots" adjusted_gene_expression_plots: type: File? format: "http://edamontology.org/format_3508" outputSource: estimate_contamination/adjusted_gene_expression_plots label: "Adjusted gene expression plots" doc: "Adjusted gene expression plots" raw_gene_expression_to_pure_soup_ratio_plots: type: File? format: "http://edamontology.org/format_3508" outputSource: estimate_contamination/raw_gene_expression_to_pure_soup_ratio_plots label: "Raw gene expression to pure soup ratio plots" doc: "Raw gene expression to pure soup ratio plots" raw_to_adjusted_gene_expression_ratio_plots: type: File? format: "http://edamontology.org/format_3508" outputSource: estimate_contamination/raw_to_adjusted_gene_expression_ratio_plots doc: "Raw to adjusted gene expression ratio plots" soupx_stdout_log: type: File format: "http://edamontology.org/format_2330" outputSource: estimate_contamination/soupx_stdout_log label: "SoupX stdout log" doc: "SoupX stdout log" soupx_stderr_log: type: File format: "http://edamontology.org/format_2330" outputSource: estimate_contamination/soupx_stderr_log label: "SoupX stderr log" doc: "SoupX stderr log" steps: estimate_contamination: run: ../tools/soupx-subworkflow.cwl in: raw_feature_bc_matrices_folder: raw_feature_bc_matrices_folder filtered_feature_bc_matrix_folder: filtered_feature_bc_matrix_folder secondary_analysis_report_folder: secondary_analysis_report_folder genelist_file: genelist_file expression_threshold: expression_threshold fdr: fdr round_counts: round_counts out: - adjusted_feature_bc_matrices_folder - adjusted_feature_bc_matrices_h5 - contamination_estimation_plot - raw_gene_expression_plots - adjusted_gene_expression_plots - raw_gene_expression_to_pure_soup_ratio_plots - raw_to_adjusted_gene_expression_ratio_plots - soupx_stdout_log - soupx_stderr_log $namespaces: s: http://schema.org/ $schemas: - https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf s:name: "SoupX Estimate" label: "SoupX Estimate" s:alternateName: "Estimates and removes cell free mRNA contamination for Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments" s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/soupx.cwl s:codeRepository: https://github.com/datirium/workflows s:license: http://www.apache.org/licenses/LICENSE-2.0 s:isPartOf: class: s:CreativeWork s:name: Common Workflow Language s:url: http://commonwl.org/ s:creator: - class: s:Organization s:legalName: "Cincinnati Children's Hospital Medical Center" s:location: - class: s:PostalAddress s:addressCountry: "USA" s:addressLocality: "Cincinnati" s:addressRegion: "OH" s:postalCode: "45229" s:streetAddress: "3333 Burnet Ave" s:telephone: "+1(513)636-4200" s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" s:department: - class: s:Organization s:legalName: "Allergy and Immunology" s:department: - class: s:Organization s:legalName: "Barski Research Lab" s:member: - class: s:Person s:name: Michael Kotliar s:email: mailto:misha.kotliar@gmail.com s:sameAs: - id: http://orcid.org/0000-0002-6486-3898 doc: | SoupX Estimate ==============