@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix Parameter: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
cwl:source .
rdfs:comment "name used for the html report and the corresponding zip file" ;
cwl:default "multiqc" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--filename"
] ;
sld:type xsd:string .
rdfs:comment "Filter by distance beiween matepairs.\nUse \"unknown\" to find matepairs split\nbetween the references. Use from-to to limit\nmatepair distance on the same reference\n" ;
cwl:inputBinding [ CommandLineBinding:position 14 ;
CommandLineBinding:prefix "--matepair-distance"
] ;
sld:type , sld:null .
cwl:in ;
cwl:out , ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self)_fastqc.html" .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"NanoPlot_*.log" ] ;
sld:type cwl:File .
rdfs:comment "reads to be checked in sam format" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.accession)/$(inputs.accession).sra" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self).bam" .
cwl:in , , ;
cwl:out , , ;
cwl:run .
rdfs:comment "Minimum spot id\n" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--minSpotId"
] ;
sld:type xsd:string , sld:null .
Parameter:streamable true ;
cwl:outputBinding [ CommandOutputBinding:glob
"output.sam" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
rdfs:comment "Split spots into individual reads\n" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--split-spot"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"NanoStats.txt" ] ;
sld:type cwl:File .
rdfs:comment "Filter by sequence length >= \n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--minReadLen"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--N50" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Specifies a non-default file which contains the list of\ncontaminants to screen overrepresented sequences against.\nThe file must contain sets of named contaminants in the\nform name[tab]sequence. Lines prefixed with a hash will\nbe ignored.\n" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--contaminants"
] ;
sld:type cwl:File , sld:null .
cwl:in , ;
cwl:out , , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*.html" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "This CWL file defines running minimap2 to align some sequences to a database. We assume the database has been indexed. This is not necessary but we will do it in our use case" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o" "output.sam" ) ;
cwl:baseCommand ( "minimap2" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "minimap2" ;
SoftwarePackage:specs "https://github.com/lh3/minimap2" ;
SoftwarePackage:version "2.16"
]
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ttubb/minimap2:release-0.2.0"
] ;
cwl:inputs , , , , ;
cwl:outputs .
cwl:inputBinding [ CommandLineBinding:prefix
"--colormap" ] ;
sld:type xsd:string , sld:null .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sra_file.nameroot).fastq" , "$(inputs.sra_file.nameroot)_1.fastq" ] ;
sld:type cwl:File .
rdfs:comment "Files come from raw casava output. Files in the same sample\ngroup (differing only by the group number) will be analysed\nas a set rather than individually. Sequences with the filter\nflag set in the header will be excluded from the analysis.\nFiles must have the same names given to them by casava\n(including being gzipped and ending with .gz) otherwise they\nwon't be grouped together correctly.\n" ;
cwl:inputBinding [ CommandLineBinding:position 13 ;
CommandLineBinding:prefix "--casava"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string .
rdfs:comment "Transport protocol to use 'fasp', 'http' or 'both'\n" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-t"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Filter used in early 1000 Genomes data: no sequences starting or ending with >= 10N\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "--qual-filter"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--percentqual" ] ;
sld:type xsd:boolean , sld:null .
cwl:format ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq_rich" ] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--minqual" ] ;
sld:type xsd:int , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type cwl:File .
cwl:source .
sld:symbols , , , , ;
sld:type sld:enum .
rdfs:comment "Defline contains only original sequence name\n" ;
cwl:inputBinding [ CommandLineBinding:position 30 ;
CommandLineBinding:prefix "--origfmt"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"LengthvsQualityScatterPlot_kde.*" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:default true .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:symbols , ;
sld:type sld:enum .
cwl:inputBinding [ CommandLineBinding:prefix
"--summary" ] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"LengthvsQualityScatterPlot_dot.*" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"NanoPlot-report.html" ] ;
sld:type cwl:File .
cwl:format ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cram" ] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Specifies a non-default file which contains the list of\nadapter sequences which will be explicity searched against\nthe library. The file must contain sets of named adapters\nin the form name[tab]sequence. Lines prefixed with a hash\nwill be ignored.\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "--adapters"
] ;
sld:type cwl:File , sld:null .
rdfs:comment "Defline format specification for quality.\n is string of characters and/or\nvariables. The variables can be one of: $ac\n- accession, $si spot id, $sn spot\nname, $sg spot group (barcode), $sl spot\nlength in bases, $ri read number, $rn\nread name, $rl read length in bases. '[]'\ncould be used for an optional output: if\nall vars in [] yield empty values whole\ngroup is not printed. Empty value is empty\nstring or for numeric variables. Ex:\n@$sn[_$rn]/$ri '_$rn' is omitted if name\nis empty\n" ;
cwl:inputBinding [ CommandLineBinding:position 34 ;
CommandLineBinding:prefix "--defline-qual"
] ;
sld:type xsd:string , sld:null .
cwl:default "sr" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-x"
] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:comment "Tool runs fastq-dump from NCBI SRA toolkit\nSupports only file inputs.\nOutput file names are formed on the base of `sra_file` input basename.\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:name "fastq_dump" ;
cwl:baseCommand ( "fastq-dump" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "sra-tools" ;
SoftwarePackage:specs "http://identifiers.org/biotools/sra-tools" ;
SoftwarePackage:version "2.8.2"
]
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/sratoolkit:v2.8.2-1"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs , , .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sam.nameroot).bam" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--font_scale" ] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--title" ] ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Merge multiple BAM files.\n" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "samtools" "merge" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 20000
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs .
cwl:inputBinding [ CommandLineBinding:prefix
"--listcolors" ] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n return \"*/summary.txt\";\n}\n" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--readtype" ] ;
sld:type sld:null ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.zip" ] ;
sld:type cwl:File .
cwl:format ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq_minimal" ] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Run multiqc on log files from supported bioinformatic tools.\n26/04/2020: Fixed output filenames, added support for a single input file in qc_files_array (Miguel Boland)\n" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "--zip-data-dir"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--outdir" ;
cwl:valueFrom "$(runtime.outdir)"
]
[ CommandLineBinding:position 4 ;
cwl:valueFrom "$(runtime.outdir)"
]
) ;
cwl:baseCommand ( "multiqc" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 10000
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kerstenbreuer/multiqc:1.7"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${// script merges the to input arrays\n // into one array that fulfills the type \n // requirement for \"listing\", which is\n // \"{type: array, items: [File, Directory]}\"\n\n var qc_files_array = inputs.qc_files_array;\n var qc_files_array_of_array = inputs.qc_files_array_of_array;\n var output_array = [];\n\n // add items of the qc_files_array to the output_array\n if ( qc_files_array != null ){\n // Fix to allow single qc_file_array\n if (qc_files_array.length === undefined){\n output_array.push(qc_files_array)\n } else {\n for (var i=0; i
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sra_file.nameroot)_2.fastq" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "If running with --casava then don't remove read flagged by\ncasava as poor quality when performing the QC analysis.\n" ;
cwl:inputBinding [ CommandLineBinding:position 14 ;
CommandLineBinding:prefix "--nofilter"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:valueFrom "merged.bam" .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:valueFrom "$(true)" .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Bypasses the normal sequence file format detection and\nforces the program to use the specified format. Valid\nformats are bam,sam,bam_mapped,sam_mapped and fastq\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--format"
] ;
sld:type , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:valueFrom "$(true)" .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--downsample" ] ;
sld:type xsd:int , sld:null .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-a"
] ;
sld:type xsd:boolean .
rdfs:comment "Dump only biological reads\n" ;
cwl:inputBinding [ CommandLineBinding:position 15 ;
CommandLineBinding:prefix "--skip-technical"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Number of processors to use" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--threads"
] ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--threads"
] ;
sld:type xsd:int , sld:null .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Bam to fastq conversion\n" ;
ns2:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "samtools" "fastq" ) ;
cwl:baseCommand ( "samtools" "fastq" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 20000
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 20000
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.bam_sorted)"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.bam_sorted)"
] ;
cwl:stdout "${\n if (self){\n var val = self.fastq;\n } else {\n var val = inputs.bam_sorted.nameroot;\n }\n return val + '.fastq'\n}\n" .
cwl:inputBinding [ CommandLineBinding:prefix
"--maxlength" ] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--drop_outliers" ] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type cwl:File ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Input file\n" ;
cwl:inputBinding [ CommandLineBinding:position
60 ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--no-N50" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Specifies the length of Kmer to look for in the Kmer content\nmodule. Specified Kmer length must be between 2 and 10. Default\nlength is 7 if not specified.\n" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "--kmers"
] ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Convert SAM to BAM.\n" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "-h"
]
[ CommandLineBinding:position 1 ;
cwl:valueFrom "-b"
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 10000
] ;
cwl:inputs ;
cwl:outputs ;
cwl:stdout "$(inputs.sam.nameroot).bam" .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self).fastq" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--barcoded" ] ;
sld:type xsd:boolean , sld:null .
a cwl:ExpressionTool ;
rdfs:comment "Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file\nor https://www.commonwl.org/user_guide/misc/#rename-an-output-file\n" ;
ns2:original_cwlVersion "v1.2" ;
ExpressionTool:expression "${\n inputs.srcfile.basename = inputs.newname;\n return {\"outfile\": inputs.srcfile};\n }\n" ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a