@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@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 SoftwarePackage: <https://w3id.org/cwl/cwl#SoftwarePackage/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix SoftwareRequirement: <https://w3id.org/cwl/cwl#SoftwareRequirement/> .
@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/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__lane>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__pu>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#sentinel_outputs>
        cwl:default       "process_alignment_rec:files;config__algorithm__quality_format;align_split" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_inputs>
        cwl:default       "alignment_rec:record,process_alignment_rec:record" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#postprocess_variants/batch_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#config__algorithm__seq2c_bed_ready>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/files>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#files> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "prep_samples_to_rec" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#sentinel_inputs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/reference__bwa__indexes>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__cosmic>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__validate>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "variantcall_batch_region" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-vc" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-vc"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vardict-java" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vardict-java"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vcfanno" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vcfanno"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bcftools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bcftools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vcflib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vcflib"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "pythonpy" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/pythonpy"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bedtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bedtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "gatk-framework" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/gatk-framework"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "platypus-variant" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/platypus-variant"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vardict" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vardict"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "samtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/samtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "gatk" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/gatk"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vt" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vt"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "r" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/r" ;
                                                                   SoftwarePackage:version  "3.2.2"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "picard" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/picard"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "varscan" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/varscan"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "perl" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/perl"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "freebayes" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/freebayes" ;
                                                                   SoftwarePackage:version  "1.1.0"
                                                                 ]
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#region_toolinput> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#vrn_file_region> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#region> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__lane>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#genome_build>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions_merged>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/align_bam>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/align_bam> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#sentinel_parallel>
        cwl:default       "multi-parallel" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#sentinel_outputs>
        cwl:default       "config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#vrn_file>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/align_bam_toolinput>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/align_bam> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#sentinel_inputs>
        cwl:default       "files:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__mark_duplicates:var,description:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__qc>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/description>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "process_alignment" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-align" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-align"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   8 ;
                                   ResourceRequirement:outdirMin  174610799362 ;
                                   ResourceRequirement:ramMin     24576 ;
                                   ResourceRequirement:tmpdirMin  174610798338
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "sambamba" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/sambamba"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "biobambam" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/biobambam"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "samblaster" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/samblaster"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "sentieon" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/sentieon"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "snap-aligner" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/snap-aligner" ;
                                                                   SoftwarePackage:version  "1.0dev.97"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "fgbio" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/fgbio"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bwakit" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bwakit"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bwa" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bwa"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "umis" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/umis"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "seqtk" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/seqtk"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "novoalign" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/novoalign"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "samtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/samtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "grabix" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/grabix"
                                                                 ]
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_parallel> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#hla__fastq> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#work_bam_plus__disc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#work_bam> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__lane>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__lane> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#regions__nblock>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__recalibrate>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_outputs>
        cwl:default       "vrn_file" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/alignment_rec> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/hla__fastq> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/work_bam_plus__disc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/align_bam> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/alignment_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__pl>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/config__algorithm__validate_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/work_bam>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#sentinel_inputs>
        cwl:default       "postprocess_alignment_rec:record" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#config__algorithm__variant_regions_orig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcriptome_index__tophat>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/analysis>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#analysis> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/validate__summary>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/regions__callable>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/regions__callable> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#reference__fasta__base>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary/qcout_rec> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary/summary__multiqc> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__recalibrate>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__variant_regions_merged>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__sample>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#align_bam_toolinput>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__qsignature>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__pu>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec/reference__fasta__base> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__validate_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage_merged>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__coverage_merged> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_parallel>
        cwl:default       "single-merge" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_inputs>
        cwl:default       "alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "merge_split_alignments" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "samtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/samtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "biobambam" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/biobambam"
                                                                 ]
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   8 ;
                                   ResourceRequirement:outdirMin  349221597700 ;
                                   ResourceRequirement:ramMin     24576 ;
                                   ResourceRequirement:tmpdirMin  349221596676
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-align" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-align"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__sr_toolinput> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#hla__fastq_toolinput> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#align_bam_toolinput> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__disc_toolinput> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#hla__fastq> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__disc> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#variantcall> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summarize_grading_vc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__svcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__archive> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__lcr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_hapmap> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__lb> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__realign> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcripts_mask> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__align_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__version> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__sex> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__qc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_indels> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__qsignature> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__viral> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__rg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__effects> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcriptome_index__tophat> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__dexseq> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__ensembl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__nomap_split_targets> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__refflat> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__nomap_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__sv_repeat> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__human> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_omni> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#vrn_file> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__snpeff> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcripts> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__ensemble__numpass> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_1000g> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__recalibrate> ;
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                                 ] ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__sample>
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__sr_toolinput>
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                            ] .

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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec/process_alignment_rec/config__algorithm__quality_format>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__rg>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage>
        sld:type  cwl:File , sld:null .

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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__variant_regions>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/config__algorithm__variant_regions> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate_regions>
        sld:type  sld:null .

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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#metadata__phenotype>
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                  ] .

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        sld:type  sld:null .

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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/description>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> .

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                                   ]
                                 ) ;
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                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-align" ;
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                                 ] ;
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                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bedtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bedtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "pythonpy" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/pythonpy"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ]
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
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                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/config__algorithm__aligner>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#genome_resources__variation__dbsnp>
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                  ] .

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                               ] ;
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        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#reference__genome_context>
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                               ] ;
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                  ] .

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        sld:type  cwl:File .

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        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__version>
        sld:type  [ sld:items  xsd:long ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "pipeline_summary" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bedtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bedtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "qsignature" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/qsignature"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "samtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/samtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "pythonpy" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/pythonpy"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "goleft" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/goleft"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "fastqc" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/fastqc"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "sambamba" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/sambamba"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "qualimap" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/qualimap"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bcftools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bcftools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "picard" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/picard"
                                                                 ]
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-qc" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-qc"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   8 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     24576
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#sentinel_inputs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm/vrn_file>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#postprocess_variants/vrn_file> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#sentinel_outputs>
        cwl:default       "batch_rec:description;config__algorithm__validate;reference__fasta__base;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__validate_regions;genome_build;reference__rtg;metadata__phenotype;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__cosmic;reference__genome_context;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;regions__callable;config__algorithm__callable_regions" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/description> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/reference__fasta__base>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__fasta__base> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__callable_regions>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#validate__grading_plots>
        sld:type  [ sld:items  [ sld:items  cwl:File , sld:null ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__fn>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/description> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/prep_samples_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__seq2c_bed_ready> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__recalibrate> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/postprocess_alignment_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#work_bam_plus__disc>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__validate>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#postprocess_variants/vrn_file_toolinput>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/vrn_file> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__lane>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/description>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "concat_batch_variantcalls" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-vc" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-vc"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bcftools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bcftools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ]
                                 ] ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__lb> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__rg> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__seq2c_bed_ready>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_inputs>
        cwl:default       "regions__callable:var,regions__nblock:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,description:var" ;
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                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm/vrn_file> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm/batch_rec> ;
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        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions_orig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_interval>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__ensembl>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/reference__bwa__indexes>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__qc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/reference__fasta__base> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/qc_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__coverage>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/config__algorithm__coverage> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__variant_regions_orig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/description>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#sentinel_outputs>
        cwl:default       "prep_samples_rec:description;reference__fasta__base;config__algorithm__variant_regions" ;
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                                    ";;" ;
                            CommandLineBinding:position  1 ;
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                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#description>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__recalibrate>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__sample>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/process_alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs/process_alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/vrn_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#align_bam>
        cwl:outputSource  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/align_bam> ;
        sld:type          [ sld:items  cwl:File ;
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                          ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_inputs>
        cwl:default       "align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,reference__fasta__base:var,description:var" ;
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                                    ";;" ;
                            CommandLineBinding:position  2 ;
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                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__coverage_interval>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__pu>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#process_alignment_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#process_alignment_rec/process_alignment_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/summary__qc>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_1000g>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#sentinel_inputs>
        cwl:default       "batch_rec:record,vrn_file:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/batch_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/region> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/vrn_file_region> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/vrn_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__variantcaller>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
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                               ] ;
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                  ] .

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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__callable_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__sex>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__rg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#vrn_file_toolinput>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/config__algorithm__callable_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__tp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__fn> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__fp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__summary> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__variant_regions_orig>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__validate_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__dexseq>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/analysis>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#analysis> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__callable_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments>
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        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/work_bam_plus__disc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/hla__fastq> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/align_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_interval>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__align_split_size>
        sld:type  [ sld:items  sld:null ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#sentinel_outputs>
        cwl:default       "vc_rec:validate__summary;validate__tp;validate__fp;validate__fn;description;vrn_file;config__algorithm__validate;reference__fasta__base;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__validate_regions;genome_build;reference__rtg;metadata__phenotype;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__cosmic;reference__genome_context;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;regions__callable;config__algorithm__callable_regions" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
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                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__variant_regions_merged>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__lane>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions_orig>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions_orig> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#description>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__lb>
        sld:type  [ sld:items  sld:null ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__nomap_split_targets>
        sld:type  [ sld:items  xsd:long ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__qc>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate_regions>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#sentinel_outputs>
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                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__tp>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__tools_on>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_on> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#prep_samples_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#prep_samples_rec/prep_samples_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/genome_build>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_build> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#process_alignment_rec/process_alignment_rec/config__algorithm__quality_format>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "postprocess_variants" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-vc" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-vc"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "snpeff" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/snpeff" ;
                                                                   SoftwarePackage:version  "4.3i"
                                                                 ]
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   8 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     24576
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#vrn_file_toolinput> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#vrn_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__coverage_interval>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#sentinel_parallel>
        cwl:default       "multi-combined" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#align_bam>
        cwl:secondaryFiles  []  ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#work_bam_plus__disc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#hla__fastq> ;
        cwl:requirements         [ a                         cwl:EnvVarRequirement ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "MPLCONFIGDIR" ;
                                                               EnvironmentDef:envValue  "."
                                                             ]
                                 ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/region_toolinput>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions/region> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__tp>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions_merged>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#region>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/config__algorithm__aligner>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#config__algorithm__mark_duplicates>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__rg>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__rg> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#summary__multiqc>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#metadata__batch>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec>
        sld:type  [ sld:items  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec> ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/genome_resources__variation__cosmic>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__cosmic> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_off>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary/qc_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/qc_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions/batch_rec> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions/region> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/align_bam>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/align_bam> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_outputs>
        cwl:default       "postprocess_alignment_rec:description;reference__fasta__base;config__algorithm__coverage_interval;config__algorithm__recalibrate;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs/alignment_rec> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs/process_alignment_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__variantcaller>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__variantcaller> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_inputs>
        cwl:default       "align_bam:var,analysis:var,reference__fasta__base:var,genome_build:var,config__algorithm__coverage_interval:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__qc:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,description:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/reference__bwa__indexes>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__disc_toolinput>
        cwl:secondaryFiles  []  ;
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        sld:type  xsd:string .

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        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/analysis> ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl>
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                                   ]
                                 ) ;
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                                 ] ;
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                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
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                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
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                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "sambamba" ;
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                                                                 ] ;
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                                                ]
                                 ] ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/summary__metrics>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

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        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#region>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#sentinel_parallel>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcripts>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl>
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                                   ]
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                                           "deep_listing"
                                 ] ;
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                                                                 ] ;
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                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "grabix" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/grabix"
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                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__qc>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
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                               ] ;
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec>
        sld:type  [ sld:items  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec> ;
                                 sld:type   sld:array
                               ] ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
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        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__validate_regions>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#description>
        sld:type  [ sld:items  xsd:string ;
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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__fp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/vrn_file> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__tp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__fn> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__summary> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__variantcaller> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/rgnames__pl>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#work_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__recalibrate>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__non_callable_regions>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#regions__sample_callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#prep_samples_rec/prep_samples_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_parallel>
        cwl:default       "multi-combined" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#postprocess_variants> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec> ;
        cwl:requirements         [ a                         cwl:EnvVarRequirement ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "MPLCONFIGDIR" ;
                                                               EnvironmentDef:envValue  "."
                                                             ]
                                 ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_on>
        sld:type  [ sld:items  [ sld:items  sld:null ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#sentinel_outputs>
        cwl:default       "validate__grading_summary,validate__grading_plots" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/config__algorithm__mark_duplicates>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__mark_duplicates> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#description>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__variant_regions>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#sentinel_parallel>
        cwl:default       "multi-combined" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#align_bam>
        cwl:secondaryFiles  []  ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#files>
        sld:type  [ sld:items  [ sld:items  cwl:File ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/align_bam>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/align_bam> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_parallel>
        cwl:default       "batch-single" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/work_bam_plus__disc_toolinput>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam_plus__disc> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#sentinel_inputs>
        cwl:default       "batch_rec:record,vrn_file:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#sentinel_outputs>
        cwl:default       "config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,regions__highdepth" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__callable_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "multiqc_summary" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-qc" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-qc"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "multiqc" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/multiqc"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "multiqc-bcbio" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/multiqc-bcbio"
                                                                 ]
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#summary__multiqc> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#description>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#sentinel_inputs>
        cwl:default       "analysis:var,genome_build:var,align_bam:var,config__algorithm__callable_regions:var,metadata__batch:var,metadata__phenotype:var,regions__callable:var,config__algorithm__variantcaller:var,config__algorithm__coverage_interval:var,config__algorithm__variant_regions:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,description:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment/alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#sentinel_parallel>
        cwl:default       "multi-parallel" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#reference__fasta__base>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__validate_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__seq2c_bed_ready> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__recalibrate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions_orig> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__snpeff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#sentinel_inputs>
        cwl:default       "alignment_rec:record" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__seq2c_bed_ready>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__rnaseq__transcripts_mask>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/validate__summary> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/validate__tp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/validate__fp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/validate__fn> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/vrn_file> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#vrn_file_region>
        cwl:secondaryFiles  []  ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#analysis>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__lb>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "combine_sample_regions" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-align" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-align"
                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bedtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bedtools"
                                                                 ]
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__nomap_split_targets> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#regions__nblock> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__nomap_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_parallel> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__non_callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__callable_count> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#reference__fasta__base>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/reference__rtg>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__rtg> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/rgnames__pl>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#prep_samples_rec/prep_samples_rec/config__algorithm__variant_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__lb> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__rg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/description> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/description>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_parallel>
        cwl:default       "multi-combined" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_outputs>
        cwl:default       "work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#regions__callable>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "postprocess_alignment_to_rec" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__recalibrate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__variant_regions_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__seq2c_bed_ready> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#description> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#sentinel_outputs>
        cwl:default       "summary__multiqc" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__coverage_merged>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/config__algorithm__coverage_merged> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#validate__grading_summary>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__fasta__base>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__variant_regions>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_parallel>
        cwl:default       "multi-combined" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/config__algorithm__aligner>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/prep_samples_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples_to_rec/prep_samples_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl#prep_samples_rec/prep_samples_rec/config__algorithm__variant_regions>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#hla__fastq_toolinput>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:items  [ sld:items  cwl:File ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__recalibrate>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__recalibrate> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#genome_build>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#align_bam>
        cwl:secondaryFiles  []  ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__sample>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__variant_regions>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/batch_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/region_toolinput> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/region> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/vrn_file_region> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/region_toolinput> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#config__algorithm__aligner>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/regions__callable> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/batch_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__rg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__lb> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/reference__fasta__base> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/rgnames__lb>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__seq2c_bed_ready>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__pu>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/rgnames__pu>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#sentinel_inputs>
        cwl:default       "prep_samples_rec:record" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/rgnames__lane>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#prep_align_inputs/alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/validate__fp>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summary__multiqc>
        cwl:outputSource  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary/summary__multiqc> ;
        sld:type          [ sld:items  cwl:File , sld:null ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/config__algorithm__validate>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summarize_grading_vc>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summarize_grading_vc/vc_rec> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summarize_grading_vc/validate__grading_plots> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#summarize_grading_vc/validate__grading_summary> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/process_alignment_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/alignment_rec> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam_plus__disc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam_plus__sr> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/hla__fastq> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/process_alignment_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/batch_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#config__algorithm__variant_regions_merged>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec/process_alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "batch_for_variantcall" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__variantcaller> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/reference__rtg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/metadata__phenotype> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__mark_duplicates>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#hla__fastq>
        sld:type  cwl:File , sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__tools_off>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_off> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/validate__fp>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#get_parallel_regions/batch_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__batch>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__coverage_interval>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__coverage_interval> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#analysis>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__tools_off>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__tools_off> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/summary__qc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__qc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/summary__metrics> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/description> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__lb>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__lb> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__variantcaller> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/metadata__phenotype> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__validate_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__validate> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/reference__genome_context> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/metadata__batch> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/reference__rtg> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__svcaller>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/postprocess_alignment_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/postprocess_alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/metadata__batch>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#metadata__batch> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__tools_off>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec/process_alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_merged>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__qc>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/prep_samples_rec> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__coverage_orig> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__seq2c_bed_ready> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__coverage_merged> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/prep_samples_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "qc_to_rec" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__qc> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__variant_regions_merged> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#vrn_file_region>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/config__algorithm__qc>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#sentinel_inputs>
        cwl:default       "batch_rec:record,region:var,vrn_file_region:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#variantcall>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#variantcall/batch_rec> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#variantcall/vc_rec> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#variantcall/batch_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#process_alignment_rec/process_alignment_rec/align_split>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/rgnames__pu>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__coverage>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__nomap_split_size>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__nomap_split_size> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#sentinel_parallel>
        cwl:default       "batch-split" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__coverage>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__rtg>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/batch_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "get_parallel_regions" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#region> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__sample>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#sentinel_outputs>
        cwl:default       "region" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/metadata__batch>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__nomap_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/regions__nblock> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__nomap_split_targets> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/regions__callable> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/description> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__non_callable_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__callable_count> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#sentinel_outputs>
        cwl:default       "config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#sentinel_outputs>
        cwl:default       "align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__variant_regions>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/config__algorithm__variant_regions> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__coverage_interval>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__align_split_size>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#sentinel_outputs>
        cwl:default       "qc_rec:description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/regions__nblock>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/regions__nblock> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#config__algorithm__coverage_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/reference__fasta__base>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__fasta__base> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#alignment_rec/alignment_rec/rgnames__rg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec>
        cwl:in   <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__lb> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__rg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/config__algorithm__align_split_size> ;
        cwl:out  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/alignment_rec> ;
        cwl:run  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl>
        a                        cwl:CommandLineTool ;
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                                   ResourceRequirement:ramMin     24576
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                                 ] ;
        cwl:hints                [ a                             cwl:SoftwareRequirement ;
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                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bcftools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "pythonpy" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/pythonpy"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "vcfanno" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/vcfanno"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "rtg-tools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/rtg-tools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "htslib" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/htslib"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "bedtools" ;
                                                                   SoftwarePackage:specs    "https://anaconda.org/bioconda/bedtools"
                                                                 ] ;
                                   SoftwareRequirement:packages  [ SoftwarePackage:package  "gvcf-regions" ;
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                                                                 ]
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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl#config__algorithm__callable_count>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#reference__fasta__base>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#sentinel_parallel>
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        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#sentinel_parallel>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__dbsnp>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec/alignment_rec/config__algorithm__aligner>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__coverage_orig>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/align_bam>
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        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_resources__variation__cosmic>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__pl>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/config__algorithm__variantcaller>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#reference__fasta__base>
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        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#sentinel_parallel>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec/config__algorithm__coverage_orig>
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<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__genome_context>
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        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__viral>
        sld:type  [ sld:items  [ sld:items  sld:null ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "alignment_to_rec" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#config__algorithm__align_split_size> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#sentinel_parallel> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#config__algorithm__mark_duplicates> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__sample> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__pu> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#reference__bwa__indexes> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#files> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__rg> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__pl> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#config__algorithm__aligner> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__lane> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#rgnames__lb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl#alignment_rec> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/postprocess_alignment_rec> ;
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        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/postprocess_alignment_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_build>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#multiqc_summary/qcout_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary/qcout_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__ensemble__numpass>
        sld:type  [ sld:items  xsd:long ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#process_alignment_rec/process_alignment_rec/files>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#prep_samples_rec/prep_samples_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#vrn_file>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__realign>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/config__algorithm__variant_regions>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__sv_repeat>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__variation__train_indels>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__coverage>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__tools_off>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#genome_resources__aliases__human>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#regions__nblock>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#postprocess_alignment_rec/postprocess_alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#sentinel_parallel>
        cwl:default       "batch-parallel" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "sentinel_parallel=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#align_bam>
        cwl:outputSource    <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/align_bam> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl#regions__highdepth>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__validate>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__validate> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/reference__rtg>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#concat_batch_variantcalls/region>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#variantcall_batch_region/region> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__variant_regions_merged>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec>
        sld:type  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__variant_regions>
        sld:type  [ sld:items  cwl:File ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__qc>
        sld:type  [ sld:items  xsd:string ;
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                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl#batch_rec/batch_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary>
        cwl:in             <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary/qc_rec> ;
        cwl:out            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary/qcout_rec> ;
        cwl:run            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#pipeline_summary/qc_rec> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__variantcaller>
        sld:type  [ sld:items  [ sld:items  xsd:string ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/reference__genome_context>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#batch_rec/batch_rec/metadata__phenotype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__disc>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#compare_to_rm/batch_rec>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#batch_rec> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__validate_regions>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#qc_to_rec/config__algorithm__variant_regions_merged>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/config__algorithm__variant_regions_merged> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl#vc_rec/vc_rec/regions__callable>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#merge_split_alignments/work_bam_plus__sr_toolinput>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl#process_alignment/work_bam_plus__sr> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/config__algorithm__variant_regions_merged>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#prep_samples/config__algorithm__variant_regions_merged> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl#config__algorithm__coverage_orig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/rgnames__rg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/regions__callable>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment/regions__callable> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#alignment_to_rec/rgnames__sample>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__sample> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#description>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl#alignment_rec/alignment_rec/rgnames__lane>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#batch_rec/batch_rec/genome_resources__variation__cosmic>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#postprocess_alignment_to_rec/reference__fasta__base>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#reference__fasta__base> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#work_bam_plus__sr>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl#alignment_rec/alignment_rec/config__algorithm__aligner>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#batch_rec/batch_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#config__algorithm__coverage_interval>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     cwl:valueFrom                "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcbio_nextgen.py" "runfn" "summarize_grading_vc" "cwl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/v1.2> ;
        cwl:hints                [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  1024 ;
                                   ResourceRequirement:ramMin     3072
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerImageId
                                           "quay.io/bcbio/bcbio-base" ;
                                   DockerRequirement:dockerPull  "quay.io/bcbio/bcbio-base"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#sentinel_inputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#sentinel_outputs> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#sentinel_parallel> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#validate__grading_summary> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#validate__grading_plots> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "$(JSON.stringify(inputs))" ;
                                                  cwl:entryname  "cwl.inputs.json"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#region_toolinput>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl#vc_rec/vc_rec/config__algorithm__validate>
        sld:type  sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl#batch_rec/batch_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qc_rec/qc_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/analysis>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#process_alignment_rec/process_alignment_rec/align_split>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__callable_regions>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#combine_sample_regions/config__algorithm__callable_regions> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#sentinel_inputs>
        cwl:default       "batch_rec:record,region:var" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "sentinel_inputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/genome_build>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#rgnames__pl>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl#qcout_rec/qcout_rec/summary__qc>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#config__algorithm__tools_on>
        sld:type  [ sld:items  [ sld:items  sld:null ;
                                 sld:type   sld:array
                               ] ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl#batch_rec/batch_rec/config__algorithm__tools_on>
        sld:type  [ sld:items  sld:null ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl#sentinel_outputs>
        cwl:default       "vrn_file" ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    ";;" ;
                            CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "sentinel_outputs=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec>
        sld:fields  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__tools_on> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/align_bam> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__coverage_interval> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__tools_off> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__coverage_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/genome_build> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/analysis> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__variant_regions_merged> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/description> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__coverage> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/reference__fasta__base> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__variant_regions> , <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl#qc_rec/qc_rec/config__algorithm__qc> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl#reference__rtg>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#description>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#batch_for_variantcall/config__algorithm__validate_regions>
        cwl:source  <https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl#config__algorithm__validate_regions> .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl#vc_rec/vc_rec/align_bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl#alignment_rec/alignment_rec/reference__fasta__base>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl#qcout_rec/qcout_rec/description>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl#config__algorithm__seq2c_bed_ready>
        sld:type  [ sld:items  cwl:File , sld:null ;
                    sld:type   sld:array
                  ] .

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