@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 "Optional output trimmed log file" ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outLog)" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outRemoved)" ] ;
sld:type cwl:File .
cwl:in , , , , , , , ;
cwl:out , ;
cwl:run .
rdfs:comment "output passed sequences" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string .
rdfs:comment "Output trimmed sequences" ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outName)" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:default 5 ;
sld:type xsd:int .
rdfs:comment "output removed sequences" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-removed" ] ;
sld:type xsd:string .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:comment "detect and trim adapter sequences from reads\n>autoskewer.py -t -i -o -l \n" ;
rdfs:label "autoskewer" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "-t" ;
cwl:valueFrom "$(runtime.tmpdir)"
]
) ;
cwl:baseCommand ( "autoskewer.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.04"
] ;
cwl:inputs , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.input)"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "autoskewer.error" ;
cwl:stdout "autoskewer.log" .
sld:type cwl:File .
rdfs:comment "Optional output trimmed log" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-l" ] ;
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "$(self).100.preprocess.passed.fna" .
rdfs:comment "input sequence stats file, json format" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-stats" ] ;
sld:type cwl:File .
rdfs:comment "maximum number of ambiguity characters (Ns) in a sequence which will not be rejected" ;
cwl:default 5 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-max_ambig" ] ;
sld:type xsd:int , sld:null .
cwl:default 2e+00 ;
sld:type xsd:float .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outPassed)" ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:comment "Remove reads from fasta files based on sequence stats.\nReturn fasta files with reads passed and reads removed.\n" ;
rdfs:label "preprocess fasta" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
cwl:source .
cwl:default true ;
sld:type xsd:boolean .
cwl:source ;
cwl:valueFrom "$(self).080.adapter.trim.passed.fna" .
cwl:outputBinding [ CommandOutputBinding:glob
"filter_fasta.error" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"autoskewer.error" ] ;
sld:type cwl:File .
rdfs:comment "stddev mutliplier for calculating min / max length for rejection" ;
cwl:default 2e+00 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-deviation" ] ;
sld:type xsd:float , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"autoskewer.log" ] ;
sld:type cwl:File .
cwl:default true ;
sld:type xsd:boolean .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "flag to request filtering on ambiguity characters" ;
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"-filter_ambig" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
rdfs:comment "input fasta sequence file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-input" ] ;
sld:type cwl:File .
rdfs:comment "Input sequence file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-i" ] ;
sld:type cwl:File .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self).100.preprocess.removed.fna" .
rdfs:comment "flag to request filtering on sequence length" ;
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"-filter_ln" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Output trimmed sequences" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-o" ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"filter_fasta.log" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "filter fasta file based on sequence length and/or on number of ambiguity characters (Ns)\nskipping both filters is equivalent to copying the file, but slower\n" ;
rdfs:label "filter fasta" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "filter_fasta.pl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgrast/pipeline:4.03"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "filter_fasta.error" ;
cwl:stdout "filter_fasta.log" .