@prefix SecondaryFileSchema: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix cwl: .
@prefix Workflow: .
@prefix ResourceRequirement: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".fai" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output).kff" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "-k29" "-m128" "-okff" "-t$(runtime.cores)" "@paths.txt" "$(inputs.output)" "/tmp" ) ;
cwl:baseCommand ( "kmc" ) ;
cwl:cwlVersion ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin "$(8 * 1024)"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.reads1.path)\n$(inputs.reads2.path)" ;
cwl:entryname "paths.txt"
]
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "coolmaksat/kmc"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type xsd:string .
cwl:source .
cwl:in , , , , , , ;
cwl:out , ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "stats" "$(inputs.aligned_reads)" ) ;
cwl:baseCommand ( "samtools" ) ;
cwl:cwlVersion ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "coolmaksat/bwa-mem2-samtools"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:ramMin "$(4 * 1024)"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "$(inputs.aligned_reads.nameroot).stats" .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-f" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.aligned_reads.basename)" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".crai" ] ;
sld:type cwl:File .
sld:default "sample" ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type cwl:File , xsd:string , sld:null .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"--make_examples_extra_args" ] ;
sld:type xsd:string , sld:null .
cwl:source .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-paths" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.aligned_reads.nameroot).stats" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.1" ;
Workflow:steps , , , , , , ;
cwl:cwlVersion ;
cwl:inputs , , , , , , , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:ramMin "$(8 * 1024)"
] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.aligned_reads.nameroot + '.sorted.cram')" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--regions" ] ;
sld:type cwl:File , sld:null .
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--num_shards" ] ;
sld:default 64 ;
sld:type xsd:int .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_vcf)" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-f" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--reads" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".crai" ] ;
sld:type cwl:File .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type xsd:string .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "giraffe" "--progress" "-o" "BAM" "-P" "-L" "3000" "-t" "$(runtime.cores)" ) ;
cwl:baseCommand ( "vg" ) ;
cwl:cwlVersion ;
cwl:inputs , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 64 ;
ResourceRequirement:ramMin "$(64 * 1024)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/vg:1.54.0--h9ee0642_0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "$(inputs.output)" .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "view" "-h" "$(inputs.aligned_reads)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "|"
]
"sed" "-e" "s/GRCh38#0#//g"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "|"
]
"samtools" "sort" "-@10" "-O" "CRAM" "-T" "/tmp/readsPrefix" "-"
) ;
cwl:baseCommand ( "samtools" ) ;
cwl:cwlVersion ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.aligned_reads)"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "coolmaksat/minimap2-samtools"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:ramMin "$(4 * 1024)"
] ;
cwl:stdout "$(inputs.aligned_reads.nameroot + '.sorted.cram')" .
cwl:inputBinding [ CommandLineBinding:prefix
"-Z" ] ;
sld:type cwl:File .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type xsd:string , sld:null .
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".fai" ] ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--haplotype-name" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "index" "$(inputs.aligned_reads)" ) ;
cwl:baseCommand ( "samtools" ) ;
cwl:cwlVersion ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "coolmaksat/minimap2-samtools"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.aligned_reads)"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:ramMin "$(4 * 1024)"
] .
cwl:outputSource ;
sld:type cwl:File .
sld:default "GRCh38" ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"--kff-name" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File , xsd:string , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.ref_prefix).path_list.txt" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:baseCommand ( "/opt/deepvariant/bin/run_deepvariant" ) ;
cwl:cwlVersion ;
cwl:inputs , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "google/deepvariant:1.6.0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 64 ;
ResourceRequirement:ramMin "$(96 * 1024)"
] .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--model_type" ] ;
sld:type xsd:string .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
sld:default "min_mapping_quality=1,keep_legacy_allele_counter_behavior=true,normalize_reads=true" ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"--reference" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".fai" ] ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--index-basename" ] ;
sld:default "graph_index" ;
sld:type xsd:string .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_gvcf)" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "paths" "-x" "$(inputs.graph.path)" "-L" "-Q" "$(inputs.ref_prefix)" ) ;
cwl:baseCommand ( "vg" ) ;
cwl:cwlVersion ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 64 ;
ResourceRequirement:ramMin "$(64 * 1024)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/vg:1.54.0--h9ee0642_0"
] ;
cwl:stdout "$(inputs.ref_prefix).path_list.txt" .
cwl:inputBinding [ CommandLineBinding:prefix
"--output_gvcf" ] ;
sld:default "variants.gvcf" ;
sld:type xsd:string .
cwl:source .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--output_vcf" ] ;
sld:default "variants.vcf" ;
sld:type xsd:string .
sld:type cwl:File .