@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
rdfs:comment "List of sequences to subset input by, required with subsetSeqs option" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--list" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--list" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--list" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--list" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:source .
cwl:default true .
cwl:source .
cwl:default true .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:in , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Output sequence file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
sld:type xsd:string .
cwl:source .
rdfs:comment "Transform fastq to fasta" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq2fasta" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq2fasta" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq2fasta" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq2fasta" ] ;
sld:type xsd:boolean , sld:null .
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "Return fasta with each sequence truncated to 1024 bps" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--bowtie_truncate" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--bowtie_truncate" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--bowtie_truncate" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--bowtie_truncate" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"bowtie2.log" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output)" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self).299.screen.passed.fna" .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self.basename).ids" .
rdfs:comment "Input sequence file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "Utility tool for various sequence file transformations.\n" ;
rdfs:label "seqUtil" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "seqUtil" ) ;
cwl:baseCommand ( "seqUtil" ) ;
cwl:baseCommand ( "seqUtil" ) ;
cwl:baseCommand ( "seqUtil" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "seqUtil.error" ;
cwl:stdout "seqUtil.log" .
cwl:source ;
cwl:valueFrom "$(self.basename).truncate" .
cwl:default "h_sapiens" ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
cwl:source .
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outUnaligned)" ] ;
sld:type cwl:File , sld:null .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.error" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.error" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.error" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.error" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.basename).unaligned" .
rdfs:comment "Transform fasta to ID list, sorted by ID" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2id" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2id" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2id" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2id" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"bowtie2.error" ] ;
sld:type cwl:File .
rdfs:comment "Transform fasta to tabbed, sorted by ID" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid2tab" ] ;
sld:type xsd:boolean , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Remove sequences from specified host organism using bowtie2:\n>bowtie2 -f --reorder -p $proc --un $unalignedSequences -x $indexDir/$indexName -U $sequences > /dev/null\" \n" ;
rdfs:label "organism screening" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-f" "--reorder"
[ CommandLineBinding:prefix "-p" ;
cwl:valueFrom "$(runtime.cores)"
]
[ CommandLineBinding:prefix "-x" ;
cwl:valueFrom "$(inputs.indexDir.path)/$(inputs.indexName)"
]
) ;
cwl:baseCommand ( "bowtie2" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "bowtie2.error" ;
cwl:stdout "bowtie2.log" .
cwl:default true .
rdfs:comment "Transform fasta to tabbed" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fasta2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fasta2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fasta2tab" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fasta2tab" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Prefix for index files" ;
sld:type xsd:string .
rdfs:comment "Fasta file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-U" ] ;
sld:type cwl:File .
rdfs:comment "Directory containing index files with prefix INDEXNAME" ;
cwl:default "./" ;
sld:type cwl:Directory , sld:null .
cwl:source ;
cwl:valueFrom "$(self.basename).sort" .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:string .
rdfs:comment "write unpaired reads that didn't align to " ;
cwl:inputBinding [ CommandLineBinding:prefix
"--un" ] ;
sld:type xsd:string .
rdfs:comment "Return fasta with each sequence truncated to 1024 bps" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--subset_seqs" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--subset_seqs" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--subset_seqs" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--subset_seqs" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"seqUtil.log" ] ;
sld:type cwl:File .
cwl:source .
cwl:default true .
cwl:in , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Sort fasta file by ID" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sortbyid" ] ;
sld:type xsd:boolean , sld:null .
a cwl:Workflow ;
rdfs:comment "Remove sequences which align against a reference set using bowtie2. The references are preformatted (index files)" ;
rdfs:label "screen out taxa" ;
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:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .