cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement inputs: gem_well_labels: type: string[] doc: | Array of GEM well identifiers to be used for labeling purposes only gex_molecule_info_h5: type: File[] doc: | Array of GEX molecule-level information files in HDF5 format. Outputs from "cellranger-arc count" command. atac_fragments_file_from_count: type: File[] secondaryFiles: - .tbi doc: | Array of files containing count and barcode information for every ATAC fragment observed in the experiment in TSV format. Outputs from "cellranger-arc count" command. barcode_metrics_report: type: File[] doc: | Array of files with the ATAC and GEX read count summaries generated for every barcode observed in the experiment. Outputs from "cellranger-arc count" command. indices_folder: type: Directory doc: | Compatible with Cell Ranger ARC reference folder that includes STAR and BWA indices. Should be generated by "cellranger-arc mkref" command normalization_mode: type: - "null" - type: enum symbols: ["none", "depth"] default: "none" doc: | Library depth normalization mode threads: type: int? default: 4 doc: | Number of threads for those steps that support multithreading memory_limit: type: int? default: 20 doc: | Maximum memory used (GB). The same will be applied to virtual memory outputs: web_summary_report: type: File outputSource: aggregate_counts/web_summary_report doc: | Aggregated run summary metrics and charts in HTML format metrics_summary_report: type: File outputSource: aggregate_counts/metrics_summary_report doc: | Aggregated run summary metrics in CSV format atac_fragments_file: type: File outputSource: aggregate_counts/atac_fragments_file doc: | Count and barcode information for every ATAC fragment observed in the aggregated experiment in TSV format atac_peaks_bed_file: type: File outputSource: aggregate_counts/atac_peaks_bed_file doc: | Count and barcode information for every ATAC fragment observed in the aggregated experiment in TSV format atac_peak_annotation_file: type: File outputSource: aggregate_counts/atac_peak_annotation_file doc: | Annotations of peaks based on genomic proximity alone (for aggregated experiment). Note that these are not functional annotations and they do not make use of linkage with GEX data. secondary_analysis_report_folder: type: File outputSource: compress_secondary_analysis_report_folder/compressed_folder doc: | Compressed folder with secondary analysis results including dimensionality reduction, cell clustering, and differential expression for aggregated results filtered_feature_bc_matrix_folder: type: File outputSource: compress_filtered_feature_bc_matrix_folder/compressed_folder 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 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 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 doc: | Aggregated unfiltered feature-barcode matrices containing all barcodes in HDF5 format loupe_browser_track: type: File outputSource: aggregate_counts/loupe_browser_track doc: | Loupe Browser visualization and analysis file for aggregated results aggregation_metadata: type: File outputSource: aggregate_counts/aggregation_metadata doc: | Aggregation metadata in CSV format compressed_html_data_folder: type: File outputSource: compress_html_data_folder/compressed_folder doc: | Compressed folder with CellBrowser formatted results aggregate_counts_stdout_log: type: File outputSource: aggregate_counts/stdout_log doc: | stdout log generated by cellranger-arc aggr aggregate_counts_stderr_log: type: File outputSource: aggregate_counts/stderr_log doc: | stderr log generated by cellranger-arc aggr steps: aggregate_counts: run: ../tools/cellranger-arc-aggr.cwl in: atac_fragments_file_from_count: atac_fragments_file_from_count barcode_metrics_report: barcode_metrics_report gex_molecule_info_h5: gex_molecule_info_h5 gem_well_labels: gem_well_labels indices_folder: indices_folder normalization_mode: normalization_mode threads: threads memory_limit: memory_limit virt_memory_limit: memory_limit out: - web_summary_report - metrics_summary_report - atac_fragments_file - atac_peaks_bed_file - atac_peak_annotation_file - 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 cellbrowser_build: run: ../tools/cellbrowser-build-cellranger-arc.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 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 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 s:name: "Single-cell Multiome ATAC and RNA-Seq Aggregate" label: "Single-cell Multiome ATAC and RNA-Seq Aggregate" s:alternateName: | Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/scRNA-Seq-Analysis/main/workflows/sc-multiome-aggregate-wf.cwl s:codeRepository: https://github.com/Barski-lab/scRNA-Seq-Analysis 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: | Single-cell Multiome ATAC and RNA-Seq Aggregate =========================================================== Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments