@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.cohort_name)" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.cohort_name)" ] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type xsd:boolean .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Minimum number of sv calls needed to be merged" ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:int .
a cwl:CommandLineTool ;
rdfs:label "Run SURVIVOR to merge SV calls" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/bash" "/usr/bin/survivor_merge_helper.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/survivor-cwl:1.0.6.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 2000
] .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "Require merged SVs to be on the same strand" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
cwl:valueFrom "${\n if(inputs.same_strand){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
sld:type xsd:int .
sld:type xsd:int .
cwl:source .
cwl:default "merged_annotated.vcf" ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "Estimate distance based on the size of SV" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n if(inputs.estimate_sv_distance){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
cwl:source .
cwl:source .
rdfs:comment "Minimum size of SVs to merge" ;
cwl:inputBinding [ CommandLineBinding:position
7 ] ;
sld:type xsd:int .
sld:type xsd:boolean .
rdfs:comment "bed file containing allele frequencies for a population" ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "add population allele frequencies to a vcf" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/opt/hall-lab/python-2.7.15/bin/svtools" "afreq" "$(inputs.vcf)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "|"
]
"/opt/hall-lab/python-2.7.15/bin/svtools" "vcftobedpe" "-i" "stdin"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "|"
]
"/opt/hall-lab/python-2.7.15/bin/svtools" "varlookup" "-d" "200" "-c" "POPFREQ" "-a" "stdin" "-b" "$(inputs.sv_db)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "|"
]
"/opt/hall-lab/python-2.7.15/bin/svtools" "bedpetovcf"
) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "halllab/svtools:v0.4.0-2dc7f91"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 5000
] ;
cwl:stdout "$(inputs.cohort_name)" .
sld:type xsd:int .
a cwl:Workflow ;
rdfs:label "merge and annotate svs with population allele freq" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:source .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:boolean .
cwl:source .
rdfs:comment "vcf to add population allele frequencies to" ;
sld:type cwl:File .
rdfs:comment "Require merged SVs to be of the same type" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
cwl:valueFrom "${\n if(inputs.same_type){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
rdfs:comment "Maximum distance of variants to consider for merging" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:int .
rdfs:comment "Used to generate the output file name" ;
cwl:default "SURVIVOR-sv-merged.vcf" ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "Array of VCFs to merge SV calls of" ;
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:position 1
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:string , sld:null .
cwl:source .