@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ScatterMethod: <https://w3id.org/cwl/cwl#ScatterMethod/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastq_dir>
        rdfs:label  "Directory containing FASTQ files" ;
        sld:type    [ sld:items  cwl:Directory ;
                      sld:type   sld:array
                    ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/h5ad_secondary>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#dispersion_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dispersion_plot.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/metadata_json>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/metadata_json> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#slideseq_plot>
        rdfs:label        "Slide-seq bead plot, colored by Leiden cluster" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/slideseq_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#fastq_dir>
        rdfs:comment      "Directory containing fastq files to be evaluated" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#adj_fastq_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "adj_fastq" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#orig_fastq_dirs>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#genome_build_json>
        rdfs:label        "Genome build information in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/genome_build_json> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_annotated_h5ad>
        rdfs:label        "scVelo-annotated h5ad file, including cell RNA velocity" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/annotated_h5ad_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/h5ad_primary>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/count_matrix_h5ad> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "RNA velocity analysis via scVelo" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/scvelo_analysis.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#spliced_h5ad_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#annotated_h5ad_file> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#embedding_grid_plot> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#orig_fastq_dirs>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Assay-specific adjustment of cell barcodes" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/adjust_barcodes.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#adj_fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#metadata_json> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-barcode-adj:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#qc_report>
        rdfs:label        "Quality control report in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/qc_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_qc_results>
        rdfs:label        "Quality control metrics from Scanpy" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/scanpy_qc_results> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#alevin_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes>
        cwl:in   <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/fastq_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/adj_fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/metadata_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#orig_fastq_dirs>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#keep_all_barcodes>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells>
        cwl:in   <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/h5ad_file> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/metadata_json> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/orig_fastq_dirs> ;
        cwl:out  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/annotated_h5ad_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Dimensionality reduction and clustering" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/scanpy_entry_point.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#h5ad_file> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#umap_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#umap_density_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#dispersion_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#slideseq_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#marker_gene_plot_t_test> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#filtered_data_h5ad> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads>
        cwl:in   <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/adj_fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/orig_fastq_dirs> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/threads> ;
        cwl:out  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/trimmed_fastq_dir> ;
        cwl:run  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis>
        rdfs:label  "RNA velocity analysis via scVelo" ;
        cwl:in      <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/spliced_h5ad_file> ;
        cwl:out     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/embedding_grid_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/annotated_h5ad_file> ;
        cwl:run     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#count_matrix_h5ad>
        rdfs:label        "Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/annotated_h5ad_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#adj_fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "scRNA-seq pipeline using Salmon and Alevin" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#marker_gene_plot_t_test> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_output> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#umap_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#qc_report> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#filtered_data_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_embedding_grid_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#dispersion_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_qc_results> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#slideseq_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#count_matrix_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#raw_count_matrix> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_annotated_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#genome_build_json> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#umap_density_plot> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#fastqc_dir>
        rdfs:comment       "Individual graph files and additional data files containing the raw data from which plots were drawn." ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "fastqc_output" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#qc_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "qc_results.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#assay>
        rdfs:label  "scRNA-seq assay" ;
        sld:type    xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/threads>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#umap_plot>
        rdfs:label        "UMAP dimensionality reduction plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/umap_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#expr_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "expr.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata>
        rdfs:label  "Convert Alevin output to AnnData object in h5ad format" ;
        cwl:in      <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/alevin_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/expr_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/genome_build_json> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/raw_expr_h5ad> ;
        cwl:run     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#trimmed_fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Runs fastQC on each fastq file in fastq directory" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/fastqc_wrapper.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#threads> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#fastqc_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon_output>
        rdfs:label        "Full output of `salmon alevin`" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/output_dir> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#output_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "salmon_out" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#raw_count_matrix>
        rdfs:label        "Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/raw_expr_h5ad> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/adj_fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/adj_fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/threads>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#threads> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#genome_build_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "genome_build.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results>
        rdfs:label  "Compute QC metrics" ;
        cwl:in      <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/salmon_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/h5ad_primary> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/h5ad_secondary> ;
        cwl:out     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/scanpy_qc_results> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/qc_metrics> ;
        cwl:run     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#dispersion_plot>
        rdfs:label        "Gene expression dispersion plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/dispersion_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#spliced_h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#umap_density_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "umap_embedding_density.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon>
        rdfs:label  "Salmon Alevin, with index from GRCh38 transcriptome" ;
        cwl:in      <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/trimmed_fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/expected_cell_count> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/keep_all_barcodes> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/orig_fastq_dirs> ;
        cwl:out     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/output_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#h5ad_secondary>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#umap_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "umap_by_leiden_cluster.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#count_matrix_h5ad>
        rdfs:label        "Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/count_matrix_h5ad> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#umap_density_plot>
        rdfs:label        "UMAP dimensionality reduction plot, colored by cell density" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/umap_density_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#trimmed_fastq_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trimmed" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/expected_cell_count>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#expected_cell_count> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#marker_gene_plot_logreg>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "marker_genes_by_cluster_logreg.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification>
        cwl:in   <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/expected_cell_count> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/keep_all_barcodes> ;
        cwl:out  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/count_matrix_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/salmon_output> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/raw_count_matrix> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/genome_build_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/salmon_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/salmon_output> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/trimmed_fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/trimmed_fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#raw_expr_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "raw_expr.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/keep_all_barcodes>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#keep_all_barcodes> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#expected_cell_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#raw_count_matrix>
        rdfs:label        "Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/raw_count_matrix> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/threads>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#filtered_data_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "secondary_analysis.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#metadata_json>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--metadata_json"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/expr_h5ad> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis>
        rdfs:label  "Secondary analysis via ScanPy" ;
        cwl:in      <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/h5ad_file> ;
        cwl:out     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/dispersion_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/umap_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/slideseq_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/umap_density_plot> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/marker_gene_plot_t_test> ;
        cwl:run     <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#threads>
        rdfs:label   "Number of threads for Salmon" ;
        cwl:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir>
        rdfs:label  "Directory containing FASTQ files" ;
        sld:type    [ sld:items  cwl:Directory ;
                      sld:type   sld:array
                    ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/adjust-barcodes.cwl#metadata_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "metadata.json" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#salmon_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#marker_gene_plot_t_test>
        rdfs:label        "Cluster marker genes, t-test" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/marker_gene_plot_t_test> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/expected_cell_count>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#expected_cell_count> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#expected_cell_count>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--expected-cell-count"
                          ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#h5ad_primary>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Assay-specific annotation of cell barcodes after quantification" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/annotate_cells.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#metadata_json> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#h5ad_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#annotated_h5ad_file> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#compute_qc_results/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc>
        rdfs:label         "Run fastqc on all fastq files in fastq directory" ;
        cwl:in             <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/fastq_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/threads> ;
        cwl:out            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/fastqc_dir> ;
        cwl:run            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/fastq_dir> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Convert Alevin sparse output to anndata.AnnData object, save as h5ad" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/alevin_to_anndata.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#alevin_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#raw_expr_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#expr_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/alevin-to-anndata.cwl#genome_build_json> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#expected_cell_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Trim FASTQ files" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/trim_reads.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#adj_fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/trim-reads.cwl#trimmed_fastq_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-trim-reads:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/fastqc.cwl#threads>
        rdfs:comment      "The number of threads to use for fastqc" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Salmon quantification, FASTQ -> H5AD count matrix" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#count_matrix_h5ad> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#genome_build_json> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#raw_count_matrix> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon_output> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#annotate_cells/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_embedding_grid_plot>
        rdfs:label        "scVelo velocity embedding grid plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/embedding_grid_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/keep_all_barcodes>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#keep_all_barcodes> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc_dir>
        rdfs:label        "Directory of FastQC output files, mirroring input directory structure" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/fastqc_dir> ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#marker_gene_plot_logreg>
        rdfs:label        "Cluster marker genes, logreg method" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/marker_gene_plot_logreg> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#annotated_h5ad_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "scvelo_annotated.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#scanpy_qc_results>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "qc_results.hdf5" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#slideseq_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "spatial_pos_by_leiden_cluster.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#filtered_data_h5ad>
        rdfs:comment      "Full data set of filtered results: expression matrix, coordinates in dimensionality-reduced space (PCA and UMAP), cluster assignments via the Leiden algorithm, and marker genes for one cluster vs. rest" ;
        rdfs:label        "Full data set of filtered results" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay>
        rdfs:label  "scRNA-seq assay" ;
        sld:type    xsd:string .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#genome_build_json>
        rdfs:label        "Genome build information in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/genome_build_json> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#adjust_barcodes/assay>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_output>
        rdfs:label        "Full output of `salmon alevin`" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/salmon_output> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#keep_all_barcodes>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--keep-all-barcodes"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scanpy_analysis/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/count_matrix_h5ad> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#threads>
        rdfs:label   "Number of threads for Salmon" ;
        cwl:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scvelo-analysis.cwl#embedding_grid_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "scvelo_embedding_grid.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run Salmon Alevin tool on FASTQ input" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/salmon_wrapper.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#threads> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#assay> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#trimmed_fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/salmon.cwl#output_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/salmon-grch38:latest"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  28672
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Compute QC metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/compute_qc_metrics.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#salmon_dir> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#h5ad_primary> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#h5ad_secondary> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#qc_metrics> , <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/compute-qc-metrics.cwl#scanpy_qc_results> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#scvelo_analysis/spliced_h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#salmon_quantification/count_matrix_h5ad> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastqc/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#keep_all_barcodes>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/scanpy-analysis.cwl#marker_gene_plot_t_test>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "marker_genes_by_cluster_t_test.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification/annotate-cells.cwl#annotated_h5ad_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "expr.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#trim_reads/threads>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#threads> .

<https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#alevin_to_anndata/alevin_dir>
        cwl:source  <https://w3id.org/cwl/view/git/dfb0e2abd9980bbea86b1ce9887aac812ea47ccb/steps/salmon-quantification.cwl#salmon/output_dir> .