cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement 'sd:upstream': sc_rnaseq_sample: - "single-cell-preprocess-cellranger.cwl" inputs: alias: type: string label: "Experiment short name/Alias" sd:preview: position: 1 molecule_info_h5: type: File[] label: "scRNA-Seq Cell Ranger Experiment" doc: "Molecule-level information from individual runs of cellranger count" 'sd:upstreamSource': "sc_rnaseq_sample/molecule_info_h5" 'sd:localLabel': true gem_well_labels: type: string[] label: "scRNA-Seq Cell Ranger Experiment" doc: "Array of GEM well identifiers to be used for labeling purposes only" 'sd:upstreamSource': "sc_rnaseq_sample/alias" 'sd:localLabel': true normalization_mode: type: - "null" - type: enum symbols: ["none", "mapped"] default: "mapped" label: "Library depth normalization mode" doc: "Library depth normalization mode" 'sd:layout': advanced: true threads: type: int? default: 4 label: "Number of threads" doc: "Number of threads for those steps that support multithreading" 'sd:layout': advanced: true memory_limit: type: int? default: 30 label: "Maximum memory used (GB)" doc: "Maximum memory used (GB). The same will be applied to virtual memory" 'sd:layout': advanced: true outputs: web_summary_report: type: File outputSource: aggregate_counts/web_summary_report label: "Aggregated run summary metrics and charts in HTML format" doc: | Aggregated run summary metrics and charts in HTML format 'sd:visualPlugins': - linkList: tab: 'Overview' target: "_blank" metrics_summary_report_json: type: File outputSource: aggregate_counts/metrics_summary_report_json label: "Aggregated run summary metrics in JSON format" doc: | Aggregated run summary metrics in JSON format secondary_analysis_report_folder: type: File outputSource: compress_secondary_analysis_report_folder/compressed_folder label: "Compressed folder with aggregated secondary analysis results" doc: | Compressed folder with secondary analysis results including dimensionality reduction, cell clustering, and differential expression of aggregated results filtered_feature_bc_matrix_folder: type: File outputSource: compress_filtered_feature_bc_matrix_folder/compressed_folder label: "Compressed folder with aggregated filtered feature-barcode matrices" doc: | Compressed folder with aggregated filtered feature-barcode matrices containing only cellular barcodes in MEX format filtered_feature_bc_matrix_h5: type: File outputSource: aggregate_counts/filtered_feature_bc_matrix_h5 label: "Aggregated filtered feature-barcode matrices in HDF5 format" doc: | Aggregated filtered feature-barcode matrices containing only cellular barcodes in HDF5 format raw_feature_bc_matrices_folder: type: File outputSource: compress_raw_feature_bc_matrices_folder/compressed_folder label: "Compressed folder with aggregated unfiltered feature-barcode matrices" doc: | Compressed folder with aggregated unfiltered feature-barcode matrices containing all barcodes in MEX format raw_feature_bc_matrices_h5: type: File outputSource: aggregate_counts/raw_feature_bc_matrices_h5 label: "Aggregated unfiltered feature-barcode matrices in HDF5 format" doc: | Aggregated unfiltered feature-barcode matrices containing all barcodes in HDF5 format loupe_browser_track: type: File outputSource: aggregate_counts/loupe_browser_track label: "Loupe Browser visualization and analysis file for aggregated results" doc: | Loupe Browser visualization and analysis file for aggregated results aggregation_metadata: type: File outputSource: aggregate_counts/aggregation_metadata label: "Aggregation metadata in CSV format" doc: | Aggregation metadata in CSV format aggregate_counts_stdout_log: type: File outputSource: aggregate_counts/stdout_log label: "stdout log generated by cellranger aggr" doc: | stdout log generated by cellranger aggr aggregate_counts_stderr_log: type: File outputSource: aggregate_counts/stderr_log label: "stderr log generated by cellranger aggr" doc: | stderr log generated by cellranger aggr compressed_html_data_folder: type: File outputSource: compress_html_data_folder/compressed_folder label: "Compressed folder with CellBrowser formatted results" doc: | Compressed folder with CellBrowser formatted results html_data_folder: type: Directory outputSource: cellbrowser_build/html_data label: "Folder with not compressed CellBrowser formatted results" doc: | Folder with not compressed CellBrowser formatted results cellbrowser_report: type: File outputSource: cellbrowser_build/index_html_file label: "CellBrowser formatted Cellranger report" doc: | CellBrowser formatted Cellranger report 'sd:visualPlugins': - linkList: tab: 'Overview' target: "_blank" steps: aggregate_counts: run: ../tools/cellranger-aggr.cwl in: molecule_info_h5: molecule_info_h5 gem_well_labels: gem_well_labels normalization_mode: normalization_mode threads: threads memory_limit: memory_limit virt_memory_limit: memory_limit out: - web_summary_report - metrics_summary_report_json - secondary_analysis_report_folder - filtered_feature_bc_matrix_folder - filtered_feature_bc_matrix_h5 - raw_feature_bc_matrices_folder - raw_feature_bc_matrices_h5 - aggregation_metadata - loupe_browser_track - stdout_log - stderr_log compress_filtered_feature_bc_matrix_folder: run: ../tools/tar-compress.cwl in: folder_to_compress: aggregate_counts/filtered_feature_bc_matrix_folder out: - compressed_folder compress_raw_feature_bc_matrices_folder: run: ../tools/tar-compress.cwl in: folder_to_compress: aggregate_counts/raw_feature_bc_matrices_folder out: - compressed_folder compress_secondary_analysis_report_folder: run: ../tools/tar-compress.cwl in: folder_to_compress: aggregate_counts/secondary_analysis_report_folder out: - compressed_folder cellbrowser_build: run: ../tools/cellbrowser-build-cellranger.cwl in: secondary_analysis_report_folder: aggregate_counts/secondary_analysis_report_folder filtered_feature_bc_matrix_folder: aggregate_counts/filtered_feature_bc_matrix_folder aggregation_metadata: aggregate_counts/aggregation_metadata out: - html_data - index_html_file compress_html_data_folder: run: ../tools/tar-compress.cwl in: folder_to_compress: cellbrowser_build/html_data out: - compressed_folder $namespaces: s: http://schema.org/ $schemas: - https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf label: "Cell Ranger Aggregate" s:name: "Cell Ranger Aggregate" s:alternateName: "Aggregates data from multiple Cell Ranger Count Gene Expression experiments" s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/cellranger-aggr.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: | Cell Ranger Aggregate =====================