@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:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--fasta"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
cwl:in , , , , , , , , , , , , ;
cwl:out , ;
cwl:run .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "Sort VCF" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/sorted.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "SortVcf" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 18000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1"
] .
sld:type xsd:boolean .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.cohort_name)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
9 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"--plugin" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type cwl:File , sld:null .
rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ;
cwl:inputBinding [ CommandLineBinding:position 13 ;
CommandLineBinding:prefix "--species"
] ;
sld:type xsd:string .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--everything"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string .
cwl:source .
cwl:default "per_gene" .
cwl:source .
sld:type cwl:File , sld:null .
sld:type xsd:string , sld:null .
cwl:default false .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
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 .
sld:type xsd:int .
cwl:source .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:source .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"sorted.vcf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"SEQUENCE_DICTIONARY=" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
sld:type cwl:File .
rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "--assembly"
] ;
sld:type xsd:string .
sld:type xsd:boolean .
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 ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "halllab/svtools:v0.4.0-2dc7f91"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 5000
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "$(inputs.cohort_name)" .
rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ;
sld:type xsd:string .
rdfs:comment "Maximum distance of variants to consider for merging" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:int .
rdfs:comment "Minimum number of sv calls needed to be merged" ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:int .
sld:type xsd:string .
rdfs:comment "Require merged SVs to be on the same strand" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
cwl:valueFrom "${\n if(inputs.same_strand){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--synonyms"
] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 7 ;
cwl:valueFrom "${\n if (inputs.custom_clinvar_vcf) {\n return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n }\n else {\n return []\n }\n}\n"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
rdfs:comment "bed file containing allele frequencies for a population" ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "Ensembl Variant Effect Predictor" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o"
[ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ;
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/vep_helper-cwl:1.1.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 64000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:label "merge and annotate svs with population allele freq and vep" ;
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:SubworkflowFeatureRequirement ] .
sld:type xsd:int .
cwl:default "merged_annotated.vcf" ;
sld:type xsd:string , sld:null .
cwl:source .
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:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 2000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/survivor-cwl:1.0.6.2"
] .
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--coding_only"
] ;
sld:type xsd:boolean .
rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
sld:type xsd:string .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.cohort_name)" ] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Require merged SVs to be of the same type" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
cwl:valueFrom "${\n if(inputs.same_type){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
sld:type xsd:string .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--dir"
] ;
sld:type xsd:string .
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:source .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated.vcf" ] ;
sld:type cwl:File .
cwl:default "flag_pick" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--" ;
CommandLineBinding:separate false
] ;
sld:type sld:null ;
sld:type [ sld:symbols , , , , , , ;
sld:type sld:enum
] .
rdfs:comment "vcf to add population allele frequencies to" ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n if (inputs.custom_gnomad_vcf) {\n return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n }\n else {\n return []\n }\n}\n"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated.vcf_summary.html" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "Estimate distance based on the size of SV" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n if(inputs.estimate_sv_distance){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n"
] ;
sld:type xsd:boolean .
rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ;
cwl:inputBinding [ CommandLineBinding:position 12 ;
CommandLineBinding:prefix "--cache_version"
] ;
sld:type xsd:string .
sld:type xsd:int .
cwl:source .
rdfs:comment "Minimum size of SVs to merge" ;
cwl:inputBinding [ CommandLineBinding:position
7 ] ;
sld:type xsd:int .
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:boolean , sld:null .
sld:type xsd:boolean .