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

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#mapping_quality>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "mapq_table.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bga_bed>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bga.bed" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Bisulfite QC tools" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#output_dir> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QC_directory> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/reference>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#output_dir>
        cwl:default  "bisulfite_QC" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/files>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/mapping_quality> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/dup_report> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cpg_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bga_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cov_dist> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/base_convertion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cov_dist_cpg> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cpg_dist> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/cph_retention> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bga_bed_dup> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/read_convertion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/cpg_retention> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/strand_table> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/cpg_retention_dist> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#QCannotation>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cpg_dist>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cpg_dist_table.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/QCannotation>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bga_bed_dup>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bga_dup.bed" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#read_convertion>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "totalReadConversionRate.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution>
        cwl:in   <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/QCannotation> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/cpg_retention_dist> ;
        cwl:run  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#outdir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#cpg_retention>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "CpGRetentionByReadPos.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/bam>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#base_convertion>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "totalBaseConversionRate.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/bam>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/reference>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#QCannotation>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary>
        cwl:in   <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/QCannotation> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/strand_table> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/mapping_quality> ;
        cwl:run  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/QCannotation>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#QCannotation>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion>
        cwl:in   <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/QCannotation> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/cpg_retention> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/read_convertion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/cph_retention> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/base_convertion> ;
        cwl:run  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/bam>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#cph_retention>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "CpHRetentionByReadPos.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/bash" "directory_gatherer.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#files> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#outdir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#gathered_directory> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ubuntu:xenial"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "set -eou pipefail\n\noutdir=\"$1\"\nfiles=\"${@:2}\"\nmkdir $outdir\nchmod -R 777 $outdir\ncp -t $outdir $files\n\nexit 0\n" ;
                                                  cwl:entryname  "directory_gatherer.sh"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  1000
                                 ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#gathered_directory>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outdir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#cpg_retention_dist>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "CpGRetentionDist.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Biscuit QC: Bisulfite conversion rate." ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/bash" "/opt/biscuit/scripts/Bisulfite_QC_bisulfiteconversion.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#QCannotation> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#read_convertion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#base_convertion> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#cph_retention> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#cpg_retention> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     16000 ;
                                   ResourceRequirement:tmpdirMin  20000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/biscuit:0.3.8.2"
                                 ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/reference>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bisulfite_conversion/reference>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#reference> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/outdir>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#output_dir> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Biscuit QC: CpG Retention Distribution" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/bash" "/opt/biscuit/scripts/Bisulfite_QC_CpGretentiondistribution.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#vcf> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#QCannotation> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#cpg_retention_dist> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/biscuit:0.3.8.2"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     16000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#cpg_retention_distribution/QCannotation>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cov_dist_cpg>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "covdist_cpg_table.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_cpg_retention_distribution.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl#files>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Biscuit QC: Bisulfite conversion rate." ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/bash" "/opt/biscuit/scripts/Bisulfite_QC_Coveragestats.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#vcf> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#QCannotation> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cpg_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bga_bed_dup> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cov_dist_cpg> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cov_dist> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#bga_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#dup_report> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cpg_dist> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/biscuit:0.3.8.2"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     16000 ;
                                   ResourceRequirement:tmpdirMin  20000
                                 ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory>
        cwl:in   <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/outdir> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/files> ;
        cwl:out  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/gathered_directory> ;
        cwl:run  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/gather_to_sub_directory.cwl> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#QCannotation>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#dup_report>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dup_report.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats>
        cwl:in   <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/vcf> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bam> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/QCannotation> ;
        cwl:out  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cpg_dist> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cov_dist_cpg> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cpg_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bga_bed_dup> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bga_bed> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/dup_report> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/cov_dist> ;
        cwl:run  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#vcf> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QC_directory>
        cwl:outputSource  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#gather_to_sub_directory/gathered_directory> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#mapping_summary/QCannotation>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#QCannotation> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cov_dist>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "covdist_table.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_coverage_stats.cwl#cpg_bed>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cpg.bed" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Biscuit QC: Bisulfite conversion rate." ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/bash" "/opt/biscuit/scripts/Bisulfite_QC_mappingsummary.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#vcf> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#QCannotation> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#reference> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#strand_table> , <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#mapping_quality> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     16000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/biscuit:0.3.8.2"
                                 ] .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#coverage_stats/bam>
        cwl:source  <https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/subworkflows/bisulfite_qc.cwl#bam> .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_conversion.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/7b4b489474473c3d2d992a838b89632c2b97dc2c/definitions/tools/bisulfite_qc_mapping_summary.cwl#strand_table>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "strand_table.txt" ] ;
        sld:type           cwl:File .