@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix Parameter: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
cwl:default "2" ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "O=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "$(inputs.reference_genome.nameroot).dict"
]
) ;
cwl:baseCommand ( "picard" "CreateSequenceDictionary" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/picard:2.18.25--0"
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-M"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-p"
]
) ;
cwl:baseCommand ( "bwa" "mem" "-M" "-p" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bwa:0.7.17--h84994c4_5"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 10500 ;
ResourceRequirement:tmpdirMin 10700
] ;
cwl:stdout "$(inputs.sample_name).sam" .
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "gatk-base_recalibration_print_reads" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-dt" ;
cwl:valueFrom "NONE"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.input.nameroot).bqsr.bam"
]
) ;
cwl:baseCommand ( "java" "-jar" "/usr/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 8000
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk3:3.6-0"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.br_model)" ] ;
cwl:listing [ cwl:entry "$(inputs.dict)" ] ;
cwl:listing [ cwl:entry "$(inputs.reference_genome)" ]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "gatk3-haplotypecaller" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--num_cpu_threads_per_data_thread" ;
cwl:valueFrom "$(inputs.threads)"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-dt" ;
cwl:valueFrom "NONE"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-rf" ;
cwl:valueFrom "BadCigar"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-ERC" ;
cwl:valueFrom "GVCF"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-variant_index_type" ;
cwl:valueFrom "LINEAR"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-variant_index_parameter" ;
cwl:valueFrom "128000"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.input.nameroot).vcf.gz"
]
) ;
cwl:baseCommand ( "java" "-jar" "/usr/GenomeAnalysisTK.jar" "-T" "HaplotypeCaller" "--never_trim_vcf_format_field" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
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 "$(inputs.reference_genome)" ] ;
cwl:listing [ cwl:entry "$(inputs.dict)" ]
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk3:3.6-0"
] .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "samtools-bam_sort" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.input.nameroot).sorted.bam"
]
) ;
cwl:baseCommand ( "samtools" "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 8000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/samtools:1.3.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
12 ] ;
sld:type sld:null ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"--GVCFGQBands" ] ;
sld:items xsd:int ;
sld:type sld:array
] .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "cutadapt" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.raw_sequences[0].basename + \".trimmed.fastq.gz\")"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--overlap" ;
cwl:valueFrom "6"
]
[ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-j" ;
cwl:valueFrom "0"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--error-rate" ;
cwl:valueFrom "0.2"
]
) ;
cwl:baseCommand ( "cutadapt" "--interleaved" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/cutadapt:1.18--py36h14c3975_1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 2500 ;
ResourceRequirement:tmpdirMin 2500
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "picard-MD" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "OPTICAL_DUPLICATE_PIXEL_DISTANCE=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "100"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "TAGGING_POLICY=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "All"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "CREATE_INDEX=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "true"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "REMOVE_DUPLICATES=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "true"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "TAG_DUPLICATE_SET_MEMBERS=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "true"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "ASSUME_SORT_ORDER=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "coordinate"
]
[ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "METRICS_FILE=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "$(inputs.input.nameroot).metrics.txt"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "OUTPUT=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "$(inputs.input.nameroot).md.bam"
]
) ;
cwl:baseCommand ( "picard" "MarkDuplicates" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/picard:2.18.25--0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.sorted.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "INPUT=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-a"
] ;
sld:type cwl:File , sld:null .
cwl:default "@RG\\\\tID:H947YADXX\\\\tSM:NA12878\\\\tPL:ILLUMINA" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:source .
cwl:source .
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "samtools-faidx" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "samtools" "faidx" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 8000
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/samtools:1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.input)" ]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*.metrics.txt" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:in , , , ;
cwl:out ;
cwl:run .
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-targetIntervals"
] ;
sld:type cwl:File .
rdfs:label "picard-MD" ;
cwl:in ;
cwl:out , ;
cwl:run .
rdfs:label "gatk-base_recalibration_print_reads" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "-t INT number of threads [1]" ;
cwl:default "2" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-t"
] ;
sld:type xsd:string , sld:null .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "ir" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-dt" ;
cwl:valueFrom "NONE"
]
[ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--maxReadsForRealignment" ;
cwl:valueFrom "200000"
]
[ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.input.nameroot).realigned.bam"
]
) ;
cwl:baseCommand ( "java" "-jar" "/usr/GenomeAnalysisTK.jar" "-T" "IndelRealigner" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 8000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.dict)" ] ;
cwl:listing [ cwl:entry "$(inputs.reference_genome)" ]
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk3:3.6-0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.input.nameroot).bqsr.bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-b"
] ;
sld:type xsd:int , sld:null .
rdfs:label "gatk-haplotype_caller" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:label "gatk-ir" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.fa" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "gatk3-base_recalibration" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-dt" ;
cwl:valueFrom "NONE"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-nct" ;
cwl:valueFrom "$(inputs.threads)"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--knownSites" ;
cwl:valueFrom "$(inputs.known_indels_file)"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--knownSites" ;
cwl:valueFrom "$(inputs.unzipped_known_sites_file)"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.input.nameroot).recalibrated.grp"
]
) ;
cwl:baseCommand ( "java" "-jar" "/usr/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.dict)" ] ;
cwl:listing [ cwl:entry "$(inputs.reference_genome)" ]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7700
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk3:3.6-0"
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.dict" ] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 20 ;
CommandLineBinding:prefix "" ;
CommandLineBinding:separate false
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-BQSR"
] ;
sld:type cwl:File .
rdfs:label "gatk3-rtc" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:default "rtc_intervals.list" ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*.md.bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.trimmed.fastq.gz" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.realigned.bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--known"
] ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-c" "-v" ) ;
cwl:baseCommand ( "gunzip" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:ramMin 5000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 7500 ;
ResourceRequirement:tmpdirMin 7500
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "jlaitinen/lftpalpine"
] ;
cwl:stdout "$(inputs.reference_file[0].nameroot)" .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-c" ) ;
cwl:baseCommand ( "gunzip" ) ;
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 "jlaitinen/lftpalpine"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:outdirMin 12500 ;
ResourceRequirement:ramMin 2000 ;
ResourceRequirement:tmpdirMin 12500
] ;
cwl:stdout "$(inputs.known_sites_file.nameroot)" .
cwl:source .
sld:type cwl:File .
sld:type xsd:string , sld:null .