@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix EnvVarRequirement: <https://w3id.org/cwl/cwl#EnvVarRequirement/> .
@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 rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix EnvironmentDef: <https://w3id.org/cwl/cwl#EnvironmentDef/> .
@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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run Salmon Alevin tool on FASTQ input" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/salmon_wrapper.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#trimmed_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#output_dir> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  28672
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/salmon-grch38:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/expected_cell_count>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#expected_cell_count> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#centrality_scores_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/centrality_scores_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#metadata_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#sdata_zarr>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.zarr.zip" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/threads>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#threads> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#spatial_plot>
        rdfs:label        "Slide-seq bead plot, colored by Leiden cluster" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/spatial_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/expected_cell_count>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#expected_cell_count> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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  "v1.2" ;
        cwl:baseCommand          ( "/opt/alevin_to_anndata.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#alevin_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#expr_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#genome_build_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#raw_expr_h5ad> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#ripley_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/ripley_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#barcode_file>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/organism>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#organism> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/trimmed_fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/trimmed_fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#filtered_data_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "secondary_analysis.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_spatial_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/spatial_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#spatial_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "spatial_scatter.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Assay-specific annotation of cell barcodes after quantification" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/annotate_cells.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#metadata_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#metadata_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#img_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay>
        rdfs:label  "scRNA-seq assay" ;
        sld:type    xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_annotated_h5ad>
        rdfs:label        "scVelo-annotated h5ad file, including cell RNA velocity" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/annotated_h5ad_file> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#barcode_file>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc>
        rdfs:label         "Run fastqc on all fastq files in fastq directory" ;
        cwl:in             <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/threads> ;
        cwl:out            <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/fastqc_dir> ;
        cwl:run            <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/fastqc.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/fastq_dir> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/spliced_h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_with_ds> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run Salmon Alevin tool on FASTQ input" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/salmon_wrapper.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#trimmed_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#barcode_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#output_dir> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  28672
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/salmon-grcm39:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis>
        rdfs:label  "Secondary analysis via ScanPy" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/assay> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/deepscence_binary_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/umap_density_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/dispersion_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/deepscence_continuous_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/marker_gene_plot_t_test> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/umap_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/spatial_plot> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_continuous_plot>
        rdfs:label        "Umap with coloring by DeepScence scores" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/deepscence_continuous_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_json>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/metadata_json> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse>
        rdfs:label  "Salmon Alevin, with index from GRCm39 transcriptome" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/trimmed_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/orig_fastq_dirs> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/output_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl> ;
        cwl:when    "$(inputs.organism == 'mouse')" .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#co_occurrence_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/co_occurrence_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#marker_gene_plot_t_test>
        rdfs:label        "Cluster marker genes, t-test" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/marker_gene_plot_t_test> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/expr_h5ad> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#embedding_grid_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "scvelo_embedding_grid.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#neighborhood_enrichment_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/neighborhood_enrichment_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#genome_build_json>
        rdfs:label        "Genome build information in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/genome_build_json> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#metadata_json>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--metadata_json"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "scRNA-seq pipeline using Salmon and Alevin" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#img_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#metadata_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#organism> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#umap_density_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#sdata_zarr> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#filtered_data_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#count_matrix_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#interaction_matrix_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#co_occurrence_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_spatial_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#genome_build_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_binary_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_annotated_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#raw_count_matrix> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_output> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_embedding_grid_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_annotated_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#spatial_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_qc_results> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#centrality_scores_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#umap_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#dispersion_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#qc_report> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_continuous_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#marker_gene_plot_t_test> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#ripley_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#neighborhood_enrichment_plot> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#umap_plot>
        rdfs:label        "UMAP dimensionality reduction plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/umap_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#sdata_zarr>
        rdfs:label        "SpatialData object serialized in zarr format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/sdata_zarr> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads>
        cwl:in   <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/adj_fastq_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/trimmed_fastq_dir> ;
        cwl:run  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#keep_all_barcodes>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/secondary_matrix_path>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_with_ds> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#img_dir>
        rdfs:label  "Directory containing TIFF image data (for Visium assay)" ;
        sld:type    cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#qc_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "qc_results.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#organism>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:default       "human" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#marker_gene_plot_logreg>
        rdfs:label        "Cluster marker genes, logreg method" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/marker_gene_plot_logreg> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#squidpy_annotated_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "squidpy_annotated.h5ad" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_qc_results>
        rdfs:label        "Quality control metrics from Scanpy" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/scanpy_qc_results> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#threads>
        rdfs:label   "Number of threads for Salmon" ;
        sld:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#metadata_dir>
        rdfs:label  "Directory containing metadata, including gpr slide file (for Visium assay)" ;
        sld:type    cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#barcode_file>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "--barcode-file"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#ripley_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "ripley.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#interaction_matrix_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "interaction_matrix.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#primary_matrix_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/keep_all_barcodes>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#keep_all_barcodes> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/annotated_h5ad_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/img_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#img_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Salmon quantification, FASTQ -> H5AD count matrix" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#img_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#metadata_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon_output> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#raw_count_matrix> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#genome_build_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#count_matrix_h5ad> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/alevin_dir>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/output_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/output_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Trim FASTQ files" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/trim_reads.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#adj_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#organism>
        sld:default  "human" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/filtered_data_h5ad> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#assay_name>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#expected_cell_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#deepscence_binary_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "umap_by_deepscence_binary.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/organism>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#organism> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#qc_report>
        rdfs:label        "Quality control report in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/qc_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/adj_fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/adj_fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Identify and score scenescent cells" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/deepscence.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#h5ad_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#h5ad_with_ds> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#deepscence_plot> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#spliced_h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes>
        cwl:in   <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/fastq_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/adj_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/metadata_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification>
        cwl:in   <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/expected_cell_count> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/metadata_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/img_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/salmon_output> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/count_matrix_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/raw_count_matrix> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/genome_build_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis>
        rdfs:label  "Spatial analysis via SquidPy" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/img_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/co_occurrence_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/neighborhood_enrichment_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/spatial_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/squidpy_annotated_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/interaction_matrix_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/sdata_zarr> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/ripley_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/centrality_scores_plot> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#genome_build_json>
        rdfs:label        "Genome build information in JSON format" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/genome_build_json> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#interaction_matrix_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/interaction_matrix_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#organism>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--organism"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#output_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "salmon_out" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#salmon_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#img_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#centrality_scores_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "centrality_scores.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#dispersion_plot>
        rdfs:label        "Gene expression dispersion plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/dispersion_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#metadata_dir>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--metadata_dir"
                          ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc_dir>
        rdfs:label        "Directory of FastQC output files, mirroring input directory structure" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/fastqc_dir> ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Assay-specific adjustment of cell barcodes" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/adjust_barcodes.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl#adj_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Dimensionality reduction and clustering" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/scanpy_entry_point.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#h5ad_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#umap_density_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#marker_gene_plot_logreg> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#filtered_data_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#spatial_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#deepscence_continuous_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#dispersion_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#marker_gene_plot_t_test> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#deepscence_binary_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#umap_plot> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#threads>
        rdfs:label   "Number of threads for Salmon" ;
        sld:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/barcode_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#barcode_file> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#umap_density_plot>
        rdfs:label        "UMAP dimensionality reduction plot, colored by cell density" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/umap_density_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#organism>
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "--organism"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/img_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#img_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_embedding_grid_plot>
        rdfs:label        "scVelo velocity embedding grid plot" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/embedding_grid_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#barcode_file>
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "--barcode-file"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#h5ad_with_ds>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "expr.h5ad" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence>
        rdfs:label  "Run DeepScence method to get cell scenesense scores" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/organism> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/deepscence_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_with_ds> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#annotated_h5ad_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "scvelo_annotated.h5ad" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/alevin_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/organism> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/expr_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/genome_build_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/raw_expr_h5ad> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/expected_cell_count>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#expected_cell_count> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#metadata_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/img_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#img_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/adjust-barcodes.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/assay_name>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/organism>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#organism> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl#img_dir>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--img_dir"
                          ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/barcode_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#barcode_file> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/threads>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#co_occurrence_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "co_occurrence.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/keep_all_barcodes>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#keep_all_barcodes> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/deepscence_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "RNA velocity analysis via scVelo" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/scvelo_analysis.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#assay_name> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#spliced_h5ad_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#annotated_h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl#embedding_grid_plot> ;
        cwl:requirements         [ a                         cwl:EnvVarRequirement ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "TMPDIR" ;
                                                               EnvironmentDef:envValue  "/tmp"
                                                             ]
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/count_matrix_h5ad> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/keep_all_barcodes>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#keep_all_barcodes> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#fastqc/threads>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Dimensionality reduction and clustering" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/squidpy_entry_point.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#img_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#assay> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#centrality_scores_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#co_occurrence_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#interaction_matrix_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#sdata_zarr> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#squidpy_annotated_h5ad> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#ripley_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#neighborhood_enrichment_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#spatial_plot> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/squidpy-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#expected_cell_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#deepscence_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "deepscence.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/threads>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#threads> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#spatial_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "spatial_pos_by_leiden_cluster.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/primary_matrix_path>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_with_ds> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis>
        rdfs:label  "RNA velocity analysis via scVelo" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/assay_name> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/spliced_h5ad_file> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/embedding_grid_plot> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scvelo_analysis/annotated_h5ad_file> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scvelo-analysis.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/salmon_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/salmon_output> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#keep_all_barcodes>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#neighborhood_enrichment_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "neighborhood_enrichment.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#raw_expr_h5ad>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "raw_expr.h5ad" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells>
        cwl:in   <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/h5ad_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_json> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/img_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/annotated_h5ad_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/annotate-cells.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#trimmed_fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#adj_fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#deepscence_continuous_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "umap_by_deepscence_continuous.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/scanpy-analysis.cwl#dispersion_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dispersion_plot.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/raw_expr_h5ad> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence_binary_plot>
        rdfs:label        "Umap with coloring by DeepScence binary results" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#scanpy_analysis/deepscence_binary_plot> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_annotated_h5ad>
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/squidpy_annotated_h5ad> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.cwl#output_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "salmon_out" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/raw_count_matrix> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay>
        rdfs:label  "scRNA-seq assay" ;
        sld:type    xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#squidpy_analysis/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl#trimmed_fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/alevin-to-anndata.cwl#alevin_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/deepscence.cwl#h5ad_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/fastqc.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Runs fastQC on each fastq file in fastq directory" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/fastqc_wrapper.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/fastqc.cwl#threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/fastqc.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/fastqc.cwl#fastqc_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#count_matrix_h5ad>
        rdfs:label        "Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts, scenesence scores" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#deepscence/h5ad_with_ds> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/assay>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#assay> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#secondary_matrix_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon_output>
        rdfs:label        "Full output of `salmon alevin`" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/output_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/output_dir> ;
        cwl:pickValue     "first_non_null" ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/organism>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#organism> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#assay>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/threads>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#threads> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results>
        rdfs:label  "Compute QC metrics" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/salmon_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/primary_matrix_path> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/secondary_matrix_path> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/qc_metrics> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#compute_qc_results/scanpy_qc_results> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/squidpy-analysis.cwl#img_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/metadata_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#metadata_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Compute QC metrics" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/compute_qc_metrics.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#salmon_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#secondary_matrix_path> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#primary_matrix_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#scanpy_qc_results> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/compute-qc-metrics.cwl#qc_metrics> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:latest"
                                 ] .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon-mouse.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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/trim-reads.cwl#trimmed_fastq_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trimmed" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/organism>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#organism> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#organism>
        sld:default  "human" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/barcode_file>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#barcode_file> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/orig_fastq_dirs>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/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/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/trimmed_fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/trimmed_fastq_dir> .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_output>
        rdfs:label        "Full output of `salmon alevin`" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/pipeline.cwl#salmon_quantification/salmon_output> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon>
        rdfs:label  "Salmon Alevin, with index from GRCh38 transcriptome" ;
        cwl:in      <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/trimmed_fastq_dir> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/barcode_file> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/keep_all_barcodes> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/threads> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/assay> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/organism> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/orig_fastq_dirs> , <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/expected_cell_count> ;
        cwl:out     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/output_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification/salmon.cwl> ;
        cwl:when    "$(inputs.organism == 'human')" .