@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:prefix
"--input" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--min-base-quality" ] ;
sld:type xsd:int .
cwl:source .
cwl:source .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "call duplex consensus" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--error-rate-pre-umi" "45" "--error-rate-post-umi" "30" "--min-input-base-quality" "30" "--output"
[ cwl:valueFrom "$(runtime.outdir)/consensus_unaligned.bam" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/fgbio-0.5.0.jar" "CallDuplexConsensusReads" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/dna-alignment"
] .
cwl:outputBinding [ CommandOutputBinding:glob
"marked.bam" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "group reads by umi" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--strategy" "paired" "--assign-tag" "MI" "--raw-tag" "RX" "--min-map-q" "10" "--edits" "1" "--output"
[ cwl:valueFrom "$(runtime.outdir)/umi_grouped.bam" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/fgbio-0.5.0.jar" "GroupReadsByUmi" ) ;
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/dna-alignment"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"clipped.bam" ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:label "umi duplex alignment 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:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:Workflow ;
rdfs:label "umi per-lane alignment subworkflow" ;
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:SubworkflowFeatureRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"consensus_unaligned.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "umi realignment" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 3 ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "/bin/bash" "/usr/bin/umi_realignment.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/dna-alignment"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 16000
] .
cwl:outputBinding [ CommandOutputBinding:glob
"duplex_seq.metrics.*" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:default 5e-02 ;
sld:type xsd:float .
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "clip overlapping reads" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--soft-clip" "false" "--clip-overlapping-reads" "true" "--output"
[ cwl:valueFrom "$(runtime.outdir)/clipped.bam" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/fgbio-0.5.0.jar" "ClipBam" ) ;
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:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/dna-alignment"
] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--min-reads" ] ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out , ;
cwl:run .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"umi_grouped.bam" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref" ] ;
sld:type xsd:string .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:default 1e-01 ;
sld:type xsd:float , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"adapter_metrics.txt" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out , ;
cwl:run ;
cwl:scatter ( ) .
cwl:default 10 , 5 , 3 ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"--max-base-error-rate" ] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--intervals" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"umi_extracted.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "INPUT="
] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:string .
cwl:default 5e-02 ;
sld:type xsd:float , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
sld:type xsd:string .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "filter consensus reads" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--output"
[ cwl:valueFrom "$(runtime.outdir)/consensus_filtered.bam" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/fgbio-0.5.0.jar" "FilterConsensusReads" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/dna-alignment"
] .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "collect duplex seq metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--output"
[ cwl:valueFrom "$(runtime.outdir)/duplex_seq.metrics" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/fgbio-0.5.0.jar" "CollectDuplexSeqMetrics" ) ;
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:ramMin 6000 ;
ResourceRequirement:tmpdirMin 1000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/dna-alignment"
] .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref" ] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "fastq to bam" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "OUTPUT="
[ cwl:valueFrom "$(runtime.outdir)/marked.bam" ]
"METRICS="
[ cwl:valueFrom "$(runtime.outdir)/adapter_metrics.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/picard/picard.jar" "MarkIlluminaAdapters" ) ;
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/dna-alignment"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"--max-read-error-rate" ] ;
sld:type xsd:float , sld:null .
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"merged.bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:default 50 ;
sld:type xsd:int .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--read-structure" ] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"--max-no-call-fraction" ] ;
sld:type xsd:float , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "umi alignment" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 3 ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "/bin/bash" "/usr/bin/umi_alignment.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs