@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
cwl:valueFrom "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
]
"sentinel_parallel=single-parallel" "sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr" "sentinel_inputs=alignment_rec:record,process_alignment_rec:record"
) ;
cwl:baseCommand ( "bcbio_nextgen.py" "runfn" "process_alignment" "cwl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerImageId
"quay.io/bcbio/bcbio-align" ;
DockerRequirement:dockerPull "quay.io/bcbio/bcbio-align"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 5244 ;
ResourceRequirement:ramMin 24576 ;
ResourceRequirement:tmpdirMin 4220
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "umis" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/umis"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "bwakit" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/bwakit"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "sentieon" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/sentieon"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "grabix" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/grabix"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "novoalign" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/novoalign"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "samblaster" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/samblaster"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "bwa" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/bwa"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "fgbio" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/fgbio"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "sambamba" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/sambamba"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "samtools" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/samtools"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "seqtk" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/seqtk"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "snap-aligner" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/snap-aligner" ;
SoftwarePackage:version "1.0dev.97"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "biobambam" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/biobambam"
]
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(JSON.stringify(inputs))" ;
cwl:entryname "cwl.inputs.json"
]
] .
sld:fields , , , , , , , , , , , , ;
sld:type sld:record .
sld:type xsd:string .
sld:type xsd:string , sld:null .
sld:type xsd:string .
sld:type cwl:File .
cwl:source .
cwl:source .
sld:fields , , , , , , , , , , , , ;
sld:type sld:record .
sld:type .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string , sld:null .
sld:type xsd:string .
sld:type xsd:string , sld:null .
cwl:source .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
cwl:valueFrom "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
]
"sentinel_parallel=single-split" "sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split" "sentinel_inputs=alignment_rec:record"
) ;
cwl:baseCommand ( "bcbio_nextgen.py" "runfn" "prep_align_inputs" "cwl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerImageId
"quay.io/bcbio/bcbio-align" ;
DockerRequirement:dockerPull "quay.io/bcbio/bcbio-align"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "grabix" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/grabix"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "biobambam" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/biobambam"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "htslib" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/htslib"
]
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin 5244 ;
ResourceRequirement:ramMin 3072 ;
ResourceRequirement:tmpdirMin 4220
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(JSON.stringify(inputs))" ;
cwl:entryname "cwl.inputs.json"
]
] .
cwl:source .
sld:fields , , , , , , , , , , , , ;
sld:type sld:record .
cwl:source .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:fields , , , , , , , , , , , , ;
sld:type sld:record .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File , sld:null ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string , sld:null .
sld:type xsd:string , sld:null .
sld:type xsd:string , sld:null .
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
cwl:valueFrom "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])"
]
"sentinel_parallel=single-merge" "sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq" "sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var"
) ;
cwl:baseCommand ( "bcbio_nextgen.py" "runfn" "merge_split_alignments" "cwl" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerImageId
"quay.io/bcbio/bcbio-align" ;
DockerRequirement:dockerPull "quay.io/bcbio/bcbio-align"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 9465 ;
ResourceRequirement:ramMin 24576 ;
ResourceRequirement:tmpdirMin 8441
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "biobambam" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/biobambam"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "samtools" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/samtools"
]
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(JSON.stringify(inputs))" ;
cwl:entryname "cwl.inputs.json"
]
] .
sld:type xsd:string .
sld:type xsd:string .
sld:type cwl:File .
sld:type xsd:string , sld:null .
sld:type xsd:string .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:string .
cwl:source .
sld:type .
sld:fields , , ;
sld:type sld:record .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
sld:type .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:boolean , xsd:string , sld:null .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File , sld:null ;
sld:type sld:array
] .
sld:type xsd:boolean , xsd:string , sld:null .
sld:type xsd:string .
sld:type cwl:File .
sld:type cwl:File .
sld:type cwl:File , sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string , sld:null .
sld:type xsd:string .
sld:type xsd:string .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type xsd:string .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:boolean , xsd:string , sld:null .
sld:type xsd:string .
sld:type .
sld:type xsd:string .
sld:type xsd:string .
sld:type cwl:File .
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , ;
cwl:out , , , , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string .
cwl:source .
sld:type xsd:string .
cwl:in , , , , , ;
cwl:out , , , ;
cwl:run .
sld:type xsd:string .
sld:type [ sld:items cwl:File , sld:null ;
sld:items [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type sld:array
] .
sld:type .
sld:type xsd:string , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type cwl:File , sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:boolean , xsd:string , sld:null .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string .
sld:type [ sld:items ;
sld:type sld:array
] .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:Workflow ;
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 ] ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "MPLCONFIGDIR" ;
EnvironmentDef:envValue "."
]
] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
sld:fields , , ;
sld:type sld:record .
sld:type xsd:string .
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type xsd:string .