@prefix LoadListingRequirement: .
@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:inputBinding [ CommandLineBinding:prefix
"REFERENCE_SEQUENCE=" ] ;
sld:type xsd:string .
cwl:default true .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:default "MT" , "X" , "Y" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-ignore" ] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:int , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-2" ] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "bwa-indexed reference file" ;
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"--minFragmentLength" ] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--scaleFactor" ] ;
sld:type xsd:float , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
sld:type xsd:string .
cwl:source .
cwl:in , , ;
cwl:out , , ;
cwl:run .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"refAlign.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:default "MarkedSorted.bam" ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--maxFragmentLength" ] ;
sld:type xsd:int , sld:null .
cwl:source ;
cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" .
cwl:in ;
cwl:out ;
cwl:run .
cwl:default "ALL_READS" ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Creating the homer tag directory" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/bash" "homer_tag_directory.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:ramMin 32000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/homer:4.10"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nname=\"homer_tag_directory\"\nbam=$1\nmkdir -p $name\necho \"creating tagDir\"\n/opt/homer/bin/makeTagDirectory $name $bam\n" ;
cwl:entryname "homer_tag_directory.sh"
]
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:outputBinding [ CommandOutputBinding:glob
"homer_tag_directory" ] ;
sld:type cwl:Directory .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:default 2451960000 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--effectiveGenomeSize" ] ;
sld:type xsd:long , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:default "final.bam" ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:label "collect WGS metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).WgsMetrics.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ;
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"
] .
a cwl:CommandLineTool ;
rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ;
rdfs:label "align with bwa_mem and tag" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-n" ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 20000
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nwhile getopts \"b:?1:?2:?g:r:n:\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\n" ;
cwl:entryname "sequence_alignment_helper.sh"
]
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:stdout "refAlign.bam" .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source ;
cwl:valueFrom "base-$(self.label)" .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).sam" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--exactScaling" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample_name).GcBiasMetrics.txt" ] ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:label "a file with a label" ;
sld:fields , ;
sld:type sld:record .
cwl:source .
cwl:default "out" ;
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "$(self.readgroup)" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:int , sld:null .
cwl:source .
a cwl:Workflow ;
rdfs:label "WGS QC workflow mouse" ;
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:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:valueFrom "ALL_READS" .
cwl:inputBinding [ CommandLineBinding:prefix
"--samFlagInclude" ] ;
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:inputBinding [ CommandLineBinding:prefix
"--smoothLength" ] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).NameSorted.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:in , , ;
cwl:out , ;
cwl:run .
cwl:valueFrom "ALL_READS" .
cwl:default "RPGC" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--normalizeUsing" ] ;
sld:type [ sld:symbols , , , , ;
sld:type sld:enum
] .
cwl:inputBinding [ CommandLineBinding:prefix
"--samFlagExclude" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:string .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ;
sld:type cwl:File .
cwl:default "final" ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-g" ] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "collect insert size metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ]
"H="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs