cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement inputs: indices_folder: type: Directory doc: | Cell Ranger reference genome indices folder fastq_file_r1: type: File doc: | FASTQ file R1 (optionally compressed) fastq_file_r2: type: File doc: | FASTQ file R2 (optionally compressed) expect_cells: type: int? default: 3000 doc: | Expected number of recovered cells force_expect_cells: type: boolean? default: false doc: | Force pipeline to use the expected number of recovered cell. The value provided in expect_cells will be sent to Cell Ranger Count as --force-cells. The latter will bypass the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. include_introns: type: boolean? default: false doc: | Count reads mapping to intronic regions. This may improve sensitivity for samples with a significant amount of pre-mRNA molecules, such as nuclei. 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: count_gene_expr/web_summary_report doc: | Run summary metrics and charts in HTML format metrics_summary_report: type: File outputSource: count_gene_expr/metrics_summary_report doc: | Run summary metrics in CSV format possorted_genome_bam_bai: type: File outputSource: count_gene_expr/possorted_genome_bam_bai doc: | Indexed reads aligned to the genome and transcriptome annotated with barcode information filtered_feature_bc_matrix_folder: type: File outputSource: compress_filtered_feature_bc_matrix_folder/compressed_folder doc: | Compressed folder with filtered feature-barcode matrices containing only cellular barcodes in MEX format filtered_feature_bc_matrix_h5: type: File outputSource: count_gene_expr/filtered_feature_bc_matrix_h5 doc: | 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 unfiltered feature-barcode matrices containing all barcodes in MEX format raw_feature_bc_matrices_h5: type: File outputSource: count_gene_expr/raw_feature_bc_matrices_h5 doc: | Unfiltered feature-barcode matrices containing all barcodes in HDF5 format 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 molecule_info_h5: type: File outputSource: count_gene_expr/molecule_info_h5 doc: | Molecule-level information used by cellranger aggr to aggregate samples into larger datasets loupe_browser_track: type: File outputSource: count_gene_expr/loupe_browser_track doc: | Loupe Browser visualization and analysis file compressed_html_data_folder: type: File outputSource: compress_html_data_folder/compressed_folder doc: | Compressed folder with UCSC Cellbrowser formatted results count_gene_expr_stdout_log: type: File outputSource: count_gene_expr/stdout_log doc: | stdout log generated by cellranger count count_gene_expr_stderr_log: type: File outputSource: count_gene_expr/stderr_log doc: | stderr log generated by cellranger count steps: extract_fastq_r1: doc: | Extracts bzip2-/gzip-/zip-compressed FASTQ file run: ../tools/extract-fastq.cwl in: compressed_file: fastq_file_r1 out: - fastq_file extract_fastq_r2: doc: | Extracts bzip2-/gzip-/zip-compressed FASTQ file run: ../tools/extract-fastq.cwl in: compressed_file: fastq_file_r2 out: - fastq_file count_gene_expr: doc: | Quantifies gene expression from a single-cell RNA-Seq library run: ../tools/cellranger-count.cwl in: fastq_file_r1: extract_fastq_r1/fastq_file fastq_file_r2: extract_fastq_r2/fastq_file indices_folder: indices_folder expect_cells: source: [expect_cells, force_expect_cells] valueFrom: $(self[1]?null:self[0]) force_cells: source: [expect_cells, force_expect_cells] valueFrom: $(self[1]?self[0]:null) include_introns: include_introns threads: threads memory_limit: memory_limit virt_memory_limit: memory_limit out: - web_summary_report - metrics_summary_report - possorted_genome_bam_bai - filtered_feature_bc_matrix_folder - filtered_feature_bc_matrix_h5 - raw_feature_bc_matrices_folder - raw_feature_bc_matrices_h5 - secondary_analysis_report_folder - molecule_info_h5 - loupe_browser_track - stdout_log - stderr_log cellbrowser_build: doc: | Exports clustering results from Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments into compatible with UCSC Cell Browser format run: ../tools/cellbrowser-build-cellranger.cwl in: secondary_analysis_report_folder: count_gene_expr/secondary_analysis_report_folder filtered_feature_bc_matrix_folder: count_gene_expr/filtered_feature_bc_matrix_folder out: - html_data compress_filtered_feature_bc_matrix_folder: doc: | Creates compressed TAR file from a folder run: ../tools/tar-compress.cwl in: folder_to_compress: count_gene_expr/filtered_feature_bc_matrix_folder out: - compressed_folder compress_raw_feature_bc_matrices_folder: doc: | Creates compressed TAR file from a folder run: ../tools/tar-compress.cwl in: folder_to_compress: count_gene_expr/raw_feature_bc_matrices_folder out: - compressed_folder compress_secondary_analysis_report_folder: doc: | Creates compressed TAR file from a folder run: ../tools/tar-compress.cwl in: folder_to_compress: count_gene_expr/secondary_analysis_report_folder out: - compressed_folder compress_html_data_folder: doc: | Creates compressed TAR file from a 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: "Single-cell RNA-Seq Alignment" s:name: "Single-cell RNA-Seq Alignment" s:alternateName: "Runs Cell Ranger Count to quantify gene expression from a single-cell RNA-Seq library" s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/sc-seq-analysis/main/workflows/sc-rna-align-wf.cwl s:codeRepository: https://github.com/Barski-lab/sc-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 RNA-Seq Alignment Runs Cell Ranger Count to quantify gene expression from a single-cell RNA-Seq library.