@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
sld:type xsd:string .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:string .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:source , ;
cwl:valueFrom "$(self[0])/$(self[1].basename)" .
sld:type xsd:string .
cwl:source .
cwl:valueFrom "genomel_cohort.gatk4.genomel_all" .
cwl:source , , , , , ;
cwl:valueFrom "${\n var log_list = []\n for (var i = 0; i < self.length; i++){\n if (Array.isArray(self[i])){\n if (Array.isArray(self[i][0])){\n for (var j = 0; j < self[i][0].length; j++){\n log_list.push(self[i][0][j])\n }\n } else { log_list.push(self[i][0]) }\n } else {\n log_list.push(self[i])\n }\n }\n return log_list\n}\n" .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:source .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self.secondaryFiles[1])" .
sld:type cwl:File .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
sld:type xsd:int .
sld:type [ sld:items cwl:File , sld:null ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.job_uuid + '.' + inputs.output_prefix + '.vcf.gz')" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.job_uuid + '.' + inputs.output_prefix + '.vcf.gz')" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:source .
cwl:in , , , , , , , ;
cwl:out , , , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:string .
sld:type xsd:boolean .
cwl:source .
cwl:source .
sld:type xsd:string .
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.secondaryFiles[1])" .
sld:type xsd:int .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/usr/bin/time -f \"{\\\\\"real_time\\\\\": \\\\\"%E\\\\\", \\\\\"user_time\\\\\": %U, \\\\\"system_time\\\\\": %S, \\\\\"wall_clock\\\\\": %e, \\\\\"maximum_resident_set_size\\\\\": %M, \\\\\"average_total_mem\\\\\": %K, \\\\\"percent_of_cpu\\\\\": \\\\\"%P\\\\\"}\" -o $('aws_upload.' + inputs.input.basename + '.time.json') aws --profile $(inputs.s3_profile) --endpoint-url $(inputs.s3_endpoint) --no-verify-ssl s3 cp $(inputs.input.path) $(inputs.s3uri)"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/usr/bin/time -f \"{\\\\\"real_time\\\\\": \\\\\"%E\\\\\", \\\\\"user_time\\\\\": %U, \\\\\"system_time\\\\\": %S, \\\\\"wall_clock\\\\\": %e, \\\\\"maximum_resident_set_size\\\\\": %M, \\\\\"average_total_mem\\\\\": %K, \\\\\"percent_of_cpu\\\\\": \\\\\"%P\\\\\"}\" -o $('aws_upload.' + inputs.input.basename + '.time.json') aws --profile $(inputs.s3_profile) --endpoint-url $(inputs.s3_endpoint) --no-verify-ssl s3 cp $(inputs.input.path) $(inputs.s3uri)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "AWS_CONFIG_FILE" ;
EnvironmentDef:envValue "$(inputs.aws_config.path)"
] ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "AWS_SHARED_CREDENTIALS_FILE" ;
EnvironmentDef:envValue "$(inputs.aws_shared_credentials.path)"
]
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "registry.gitlab.com/uc-cdis/genomel-tools/awscli:1.0"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "registry.gitlab.com/uc-cdis/genomel-tools/awscli:1.0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "AWS_CONFIG_FILE" ;
EnvironmentDef:envValue "$(inputs.aws_config.path)"
] ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "AWS_SHARED_CREDENTIALS_FILE" ;
EnvironmentDef:envValue "$(inputs.aws_shared_credentials.path)"
]
] ;
cwl:stdout "output" .
cwl:source .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.0" ;
ExpressionTool:expression "${\n var trueFile = [];\n for (var i = 0; i < inputs.file_array.length; i++){\n if (inputs.file_array[i] != null){\n trueFile.push(inputs.file_array[i])\n }\n };\n return {'output': trueFile};\n}\n" ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self + '.srt')" .
sld:type xsd:int .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:source , ;
cwl:valueFrom "$(self[0])/$(self[1].secondaryFiles[0].basename)" .
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:source .
sld:type xsd:int .
cwl:in , , , , , , ;
cwl:out , ;
cwl:run .
cwl:in , , , , , ;
cwl:out , ;
cwl:run .
cwl:source .
cwl:source .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/usr/bin/time -f \"{\\\\\"real_time\\\\\": \\\\\"%E\\\\\", \\\\\"user_time\\\\\": %U, \\\\\"system_time\\\\\": %S, \\\\\"wall_clock\\\\\": %e, \\\\\"maximum_resident_set_size\\\\\": %M, \\\\\"average_total_mem\\\\\": %K, \\\\\"percent_of_cpu\\\\\": \\\\\"%P\\\\\"}\" -o $(inputs.job_uuid + '.gatk3_selectvariants.time.json') java -Xmx100G -XX:ParallelGCThreads=30 -jar /opt/GenomeAnalysisTK.jar -T SelectVariants --variant $(inputs.input_vcf.path) -R $(inputs.reference.path) -o $(inputs.output_prefix + '.filtered.site_only.vcf.gz') -select \"QUAL > 20.0\" -ef -env"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "registry.gitlab.com/uc-cdis/genomel-exome-variant-detection/genomel_variant_calling:5.0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:int .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:int .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "sed 's/\\\\\\\\n/\\\\n/g' gvcf_path.list > fixed_gvcf_path.list\n/usr/bin/time -f \"{\\\\\"real_time\\\\\": \\\\\"%E\\\\\", \\\\\"user_time\\\\\": %U, \\\\\"system_time\\\\\": %S, \\\\\"wall_clock\\\\\": %e, \\\\\"maximum_resident_set_size\\\\\": %M, \\\\\"average_total_mem\\\\\": %K, \\\\\"percent_of_cpu\\\\\": \\\\\"%P\\\\\"}\" -o $(inputs.job_uuid + '.genomel_pdc_gatk4_cohort_genotyping.time.json') python /opt/genomel_pdc_gatk4_cohort_genotyping.py --gvcf_path fixed_gvcf_path.list -j $(inputs.job_uuid) -f $(inputs.reference.path) -L $(inputs.bed_file.path) -n $(inputs.thread_count) -c $(inputs.number_of_chunks)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 30
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "registry.gitlab.com/uc-cdis/genomel-exome-variant-detection/gatk4_1_0:1.0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "${\n var paths = [];\n for (var i = 0; i < inputs.gvcf_files.length; i++){\n if (inputs.gvcf_files[i][\"nameext\"] == \".gz\"){\n paths.push(inputs.gvcf_files[i][\"path\"])\n }\n }\n return paths.join(\"\\n\")\n }\n" ;
cwl:entryname "gvcf_path.list"
]
] .
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 99 ;
CommandLineBinding:prefix "-e"
] ;
sld:type xsd:boolean .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
99 ] ;
cwl:inputBinding [ CommandLineBinding:position
99 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "I=" ;
CommandLineBinding:separate false
] ;
sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "I=" ;
CommandLineBinding:separate false
] ;
sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:string .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , , , , , ;
cwl:out , ;
cwl:run .
cwl:source .
cwl:source .
cwl:source