@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@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#> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#threads>
        rdfs:label   "Number of threads for Salmon" ;
        sld:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc_dir>
        rdfs:label        "Directory of FastQC output files, mirroring input directory structure" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/fastqc_dir> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/threads>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/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/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "bulk scRNA-seq pipeline using Salmon" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#organism> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#threads> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#expression_matrix> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon_output> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/threads>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run Salmon quant tool on FASTQ input" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/bulk_salmon_wrapper.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#threads> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#organism> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#fastq_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#output_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/salmon-grcm39:2.2.5"
                                 ] .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastq_dir>
        rdfs:label  "Directory containing FASTQ files" ;
        sld:type    cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse>
        rdfs:label  "Salmon quant 1.0.0, with index from GRCm39 transcriptome" ;
        cwl:in      <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/fastq_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/organism> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/threads> ;
        cwl:out     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/output_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl> ;
        cwl:when    "$(inputs.organism == 'mouse')" .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/organism>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#organism> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Takes gene expression vectors from several bulk RNA samples and makes them into a gene by sample matrix" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/make_expression_matrix.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl#quant_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl#expression_matrix> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:2.2.5"
                                 ] .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix/quant_dir>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/output_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/output_dir> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#output_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "out" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix>
        rdfs:label  "Make expression matrix from quant vectors" ;
        cwl:in      <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix/quant_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix/expression_matrix> ;
        cwl:run     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#organism>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run Salmon quant tool on FASTQ input" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/bulk_salmon_wrapper.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#threads> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#organism> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#output_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/salmon-grch38:2.2.5"
                                 ] .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/organism>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#organism> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#expression_matrix>
        rdfs:label        "A hd5 file containing transcript by sample matrices of TPM and number of reads" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#make_expression_matrix/expression_matrix> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/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/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/threads>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#threads> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon-mouse.cwl#threads>
        cwl:inputBinding  [ CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/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/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc>
        rdfs:label  "Run fastqc on all fastq files in fastq directory" ;
        cwl:in      <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/threads> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/fastq_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastqc/fastqc_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/fastqc.cwl> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#organism>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl#quant_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#fastq_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#organism>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl#output_dir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "out" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon_output>
        rdfs:label        "Full output of `salmon quant`" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/output_dir> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/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/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/fastqc.cwl#fastq_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/fastqc.cwl#threads> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/fastqc.cwl#fastqc_dir> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/scrna-analysis:2.2.5"
                                 ] .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk>
        rdfs:label  "Salmon quant 1.0.0, with index from GRCh38 transcriptome" ;
        cwl:in      <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/fastq_dir> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/organism> , <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/threads> ;
        cwl:out     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/output_dir> ;
        cwl:run     <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/bulk-salmon.cwl> ;
        cwl:when    "$(inputs.organism == 'human')" .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#salmon-bulk-mouse/fastq_dir>
        cwl:source  <https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/bulk-pipeline.cwl#fastq_dir> .

<https://w3id.org/cwl/view/git/fb9d16027b2e6a25a8cdd13c3bc69c2ff79b4ee7/steps/expression-matrix.cwl#expression_matrix>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "expression_matrices.h5" ] ;
        sld:type           cwl:File .