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

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#allele_specific_binding_thresholds>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--allele-specific-binding-thresholds" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/tdna_cov>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_cov> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/normalized_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/netmhc_stab>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#netmhc_stab> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/variant_type> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#indel_bam_readcount_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_indel.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_cov>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--normal-cov" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#downstream_sequence_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-d" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#epitope_lengths>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix    "-e" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:int ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#minimum_fold_change>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/reference> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/normalized_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#peptide_sequence_length>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/alleles>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#alleles> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_filtered_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_filtered_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/downstream_sequence_length>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#downstream_sequence_length> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--maximum-transcript-support-level" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level/1> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level/2> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level/3> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level/4> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level/5> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#bam_readcount_tsv>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#transcript_expression_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_filtered_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_filtered_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#minimum_fold_change>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-c" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/phased_proximal_variants_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#phased_proximal_variants_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/data_type>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#peptide_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#reference_fasta> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#phased_proximal_variants_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#gene_expression_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#allele_specific_binding_thresholds> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#rnaseq_bam> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#transcript_expression_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#downstream_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expn_val> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_threshold> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#additional_report_columns> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#prediction_algorithms> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#detect_variants_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#netmhc_stab> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#binding_threshold> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#top_score_metric> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_base_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#fasta_size> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#alleles> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#epitope_lengths> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#exclude_nas> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_method> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#minimum_fold_change> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expression_tool> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_filtered_epitopes> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_method>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--net-chop-method" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_method/20s> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_method/cterm> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/data_type>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#binding_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-b" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Normalize variants" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/normalized.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#normalized_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#netmhc_stab>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--netmhc-stab" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_vaf>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/exclude_nas>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#exclude_nas> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/expn_val>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expn_val> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/additional_report_columns>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#additional_report_columns> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#keep_tmp_files>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants/decomposed_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          -4 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_ranked_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_ranked_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_filtered_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_filtered_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_cov>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#gene_expression_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#iedb_retries>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-r" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type>
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/RNA> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/bam>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#rnaseq_bam> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#sample_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/bam> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/min_base_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/min_mapping_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/reference_fasta> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/sample> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/snv_bam_readcount_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level/1> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level/2> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level/3> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level/4> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level/5> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/peptide_sequence_length>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#peptide_sequence_length> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#alleles>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "run vt decompose" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl#decomposed_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#trna_vaf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--trna-vaf" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_all_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_all_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#exclude_nas>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--exclude-NAs" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/data_type>
        cwl:default  "RNA" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#phased_proximal_variants_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_ranked_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "combined/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_vaf>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_ranked_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_II/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_sample_name>
        cwl:default  "NORMAL" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#expression_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/expression_file>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#transcript_expression_file> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/min_mapping_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/reference_fasta> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/min_base_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/bam> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/sample> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/normalized_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/indel_bam_readcount_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#epitope_lengths>
        sld:type  sld:null ;
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#expn_val>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--expn-val" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#fasta_size>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#alleles>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/variant_type>
        cwl:default  "indel" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/epitope_lengths>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#epitope_lengths> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/data_type>
        cwl:default  "gene" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#data_type>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/indel_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/indel_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants/decomposed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/trna_vaf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_vaf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#binding_threshold>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/normalized_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name>
        cwl:default  "TUMOR" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_method>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_method/20s> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_method/cterm> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#downstream_sequence_length>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/maximum_transcript_support_level>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#maximum_transcript_support_level> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/min_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_base_quality> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/annotated_bam_readcount_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/net_chop_method>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_method> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/sample>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#sample> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/fasta_size>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#fasta_size> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#n_threads>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--n-threads" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#additional_report_columns>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-a" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#additional_report_columns/sample_name> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_cov>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#prediction_algorithms>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "run bam-readcount" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  -3 ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#min_mapping_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#sample> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#reference_fasta> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#min_base_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#snv_bam_readcount_tsv> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/bam_readcount_helper-cwl:1.0.0"
                                 ] ;
        cwl:stdout               "$(inputs.sample)_bam_readcount.tsv" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_sample_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--normal-sample-name" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#pass_only>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--pass-only" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#detect_variants_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_vaf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_vaf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_threshold>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/prediction_algorithms>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#prediction_algorithms> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/min_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#reference_fasta>
        cwl:inputBinding  [ CommandLineBinding:position
                          -5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/input_file>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/annotated_expression_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_filtered_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "combined/$(inputs.sample_name).filtered.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#trna_cov>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--trna-cov" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/sample_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expression_tool>
        cwl:default  "kallisto" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#reference_fasta> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/expression_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/expression_tool> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/data_type> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/annotated_expression_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl#decomposed_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_cov>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/expression_file>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#gene_expression_file> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#combined_ranked_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_ranked_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#phased_proximal_variants_vcf>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "-p" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#annotated_expression_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.expression.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.expression.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#snv_bam_readcount_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_snv.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/annotated_expression_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vt_decompose.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#prediction_algorithms>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#snv_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/snv_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_i_all_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_all_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#netmhc_stab>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/bam>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#tdna_vaf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--tdna-vaf" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#sample>
        cwl:inputBinding  [ CommandLineBinding:position
                          -6 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/trna_cov>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_cov> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--net-chop-threshold" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#fasta_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expn_val>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#expression_tool>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/min_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#readcount_minimum_base_quality> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/data_type>
        cwl:default  "transcript" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Add snv and indel bam-readcount files to a vcf" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/expression_tool>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expression_tool> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          -7 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/tdna_vaf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tdna_vaf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#sample_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#detect_variants_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#reference_fasta>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/expression_tool> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/expression_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_transcript_expression_data_to_vcf/annotated_expression_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/variant_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/bam_readcount_tsv> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#exclude_nas>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_vaf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--normal-vaf" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalized_vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants/decomposed_vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_all_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_I/$(inputs.sample_name).all_epitopes.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_ranked_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_ranked_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_ranked_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_I/$(inputs.sample_name).filtered.condensed.ranked.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#sample>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_cov>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#normal_cov> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#input_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#indel_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/indel_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/minimum_fold_change>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#minimum_fold_change> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/min_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_mapping_quality> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq>
        cwl:in   <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/trna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/additional_report_columns> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/top_score_metric> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/input_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/downstream_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/phased_proximal_variants_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/exclude_nas> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/peptide_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/maximum_transcript_support_level> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/tdna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/net_chop_method> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/alleles> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/prediction_algorithms> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/trna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/tdna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/expn_val> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/net_chop_threshold> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/fasta_size> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/normal_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/minimum_fold_change> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/netmhc_stab> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/epitope_lengths> ;
        cwl:out  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_i_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/combined_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_filtered_epitopes> ;
        cwl:run  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add bam_readcount info to vcf" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#data_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#bam_readcount_tsv> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vcf_annotation_tools-cwl:3.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vcf_annotation_tools-cwl:3.0.0"
                                 ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "bam_readcount workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalize_variants> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#decompose_variants> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#sample> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#reference_fasta> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_base_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#min_mapping_quality> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#normalized_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#indel_bam_readcount_tsv> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "run pVACseq" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                   [ CommandLineBinding:position  6 ;
                                     cwl:valueFrom                "--iedb-install-directory"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     cwl:valueFrom                "/opt/iedb"
                                   ]
                                   [ CommandLineBinding:position  8 ;
                                     cwl:valueFrom                "--pass-only"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "pvacseq" "run" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#binding_threshold> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#alleles> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#tdna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#pass_only> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#prediction_algorithms> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#netmhc_stab> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#top_score_metric> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#input_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#exclude_nas> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#trna_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#additional_report_columns> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#phased_proximal_variants_vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#iedb_retries> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#minimum_fold_change> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#allele_specific_binding_thresholds> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#expn_val> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_cov> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#downstream_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#maximum_transcript_support_level> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#peptide_sequence_length> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#fasta_size> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#epitope_lengths> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_threshold> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#trna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#normal_sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#tdna_vaf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#net_chop_method> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#n_threads> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#keep_tmp_files> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_ranked_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_filtered_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_all_epitopes> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_all_epitopes> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/pvactools:1.2.0"
                                 ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#rnaseq_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#combined_all_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "combined/$(inputs.sample_name).all_epitopes.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#mhc_ii_all_epitopes>
        cwl:outputSource  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/mhc_ii_all_epitopes> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/variant_type>
        cwl:default  "snv" .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#bam_readcount/reference_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/bam_readcount.cwl#reference_fasta> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_filtered_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_II/$(inputs.sample_name).filtered.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/top_score_metric>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#top_score_metric> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/snv_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/snv_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add expression info to vcf" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.expression.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.expression.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "vcf-expression-annotator" ) ;
        cwl:baseCommand          ( "vcf-expression-annotator" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#expression_file> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#vcf> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#expression_tool> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#sample_name> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#data_type> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/vcf_expression_annotator.cwl#annotated_expression_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vcf_annotation_tools-cwl:3.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vcf_annotation_tools-cwl:3.0.0"
                                 ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#min_base_quality>
        cwl:default       20 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -2 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#top_score_metric>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#top_score_metric/lowest> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#top_score_metric/median> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#sample_name>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/normalize_variants.cwl#normalized_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "normalized.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#trna_vaf>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_tumor_rna_bam_readcount_to_vcf/annotated_bam_readcount_vcf> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_ii_all_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_II/$(inputs.sample_name).all_epitopes.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#reference_fasta>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#additional_report_columns>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#additional_report_columns/sample_name> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#allele_specific_binding_thresholds>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#tdna_cov>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--tdna-cov" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#pvacseq/net_chop_threshold>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#net_chop_threshold> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#top_score_metric>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-m" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#top_score_metric/lowest> , <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#top_score_metric/median> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/bam_readcount.cwl#min_mapping_quality>
        cwl:default       0 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#peptide_sequence_length>
        cwl:default       21 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-l" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/tools/pvacseq.cwl#mhc_i_filtered_epitopes>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "MHC_Class_I/$(inputs.sample_name).filtered.tsv" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/reference_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#reference_fasta> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#add_gene_expression_data_to_vcf/expression_tool>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#expression_tool> .

<https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#tumor_rna_bam_readcount/sample>
        cwl:source  <https://w3id.org/cwl/view/git/641bdeffd942f5121e19626a094c8633386ad546/definitions/pipelines/pvacseq.cwl#sample_name> .