@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix ns3: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
cwl:default "chrM" .
a cwl:CommandLineTool ;
cwl:baseCommand ( "gunzip" ) ;
cwl:baseCommand ( "gunzip" ) ;
cwl:cwlVersion cwl:v1.0 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n return [\n {\n \"entry\": inputs.input_file,\n \"entryname\": inputs.input_file.basename,\n \"writable\": true\n }\n ]\n}\n"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n return [\n {\n \"entry\": inputs.input_file,\n \"entryname\": inputs.input_file.basename,\n \"writable\": true\n }\n ]\n}\n"
] .
cwl:source .
rdfs:comment "exon\nstring: feature type in GTF file to be used as exons for building\ntranscripts\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbGTFfeatureExon"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbGTFfeatureExon"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "List of the chromosomes to be included into the output file. If pass as string, should be comma-separated" ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type xsd:string , sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Python script to get convert TSV annotation file to BED" ;
cwl:default "import fileinput\nfor line in fileinput.input():\n if \"txStart\" in line:\n continue\n cols = line.split(\"\\t\")\n refName = cols[1]\n chrom = cols[2]\n txStart = cols[4]\n txEnd = cols[5]\n txStart1 = cols[6]\n txEnd1 = cols[7]\n try: \n name = cols[12]\n except Exception:\n name = cols[11]\n pass\n strand = cols[3]\n exonCount = cols[8]\n cdsStart = cols[9].split(',')[0:-1]\n cdsEnd = cols[10].split(',')[0:-1]\n startEndPairs = zip(cdsStart, cdsEnd)\n sizes = ','.join(map(lambda pair: str(int(pair[1])-int(pair[0])), startEndPairs))\n deltas = ','.join(map(lambda offset: str(int(offset)-int(txStart)), cdsStart))\n if 'fix' in chrom or '_' in chrom:\n continue\n output = [chrom, txStart, txEnd, name, '1000', strand, txStart1, txEnd1, '.', exonCount, sizes, deltas]\n print \"\\t\".join(output)\n" ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Reference genome FASTA file. Includes only selected chromosomes" ;
rdfs:label "Reference genome FASTA file" ;
cwl:format ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
rdfs:comment "default: 100\nint>0: length of the donor/acceptor sequence on each side of the junctions,\nideally = (mate_length - 1)\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbOverhang"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbOverhang"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type xsd:string , sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Annotation TSV file" ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Bowtie generated stderr log for genome indices" ;
rdfs:label "Bowtie stderr log genome indices" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "STAR generated genome indices folder" ;
rdfs:label "STAR genome indices" ;
cwl:outputSource ;
sld:type cwl:Directory .
rdfs:comment "Number of threads for those steps that support multithreading" ;
rdfs:label "Number of threads to run tools" ;
sld:type xsd:int , sld:null ;
ns2:layout [] .
rdfs:comment "use packed strings internally; slower, less memory\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--packed"
] ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--packed"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Reference genome FASTA file" ;
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File .
a ns1:SoftwareSourceCode ;
ns1:about "A suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format), BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants) and HTSlib (A C library for reading/writing high-throughput sequencing data).\n" ;
ns1:codeRepository "https://github.com/samtools/samtools.git" ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "Designed and implemented the\nRAZF format, an alternative indexable compression format. RAZF is no longer\nused by or provided with SAMtools. Source code remains available in older\nSAMtools 0.1.x releases and from the standalone branch in the repository.\n" ;
ns1:name "Jue Ruan"
] ;
ns1:name "Beijing Genome Institute"
] ;
ns1:creator [ a ns1:Person ;
ns1:description "updated novo2sam.pl to support gapped alignment by novoalign." ;
ns1:name "Colin Hercus"
] ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "A major contributor to the\nSAM/BAM specification. He designed and implemented the BGZF format, the\nunderlying indexable compression format for the BAM format. BGZF does\nnot support arithmetic between file offsets.\n" ;
ns1:name "Bob Handsaker"
] ;
ns1:name "Broad Institute"
] ;
ns1:creator [ a ns1:Person ;
ns1:description "contributed the header parsing library sam_header.c and sam2vcf.pl script." ;
ns1:name "Petr Danecek"
] ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "wrote most of the initial source codes of SAMtools and various converters." ;
ns1:name "Heng Li"
] ;
ns1:name "Sanger Institute"
] ;
ns1:discussionUrl "https://lists.sourceforge.net/lists/listinfo/samtools-help" , "https://lists.sourceforge.net/lists/listinfo/samtools-devel" ;
ns1:license "https://opensource.org/licenses/MIT" , "https://opensource.org/licenses/BSD-3-Clause" ;
ns1:name "samtools" ;
ns1:programmingLanguage "C, Perl" ;
ns1:publication , , ;
ns1:targetProduct [ a ns1:SoftwareApplication ;
ns1:applicationCategory "commandline tool" ;
ns1:softwareVersion "1.4"
] ;
ns1:url "http://www.htslib.org/" .
cwl:in , ;
cwl:out , , ;
cwl:run .
a ns1:ScholarlyArticle ;
ns1:name "(Li, 2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics." ;
ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/21903627" .
rdfs:comment "Genome type, such as mm10, hg19, hg38, etc" ;
rdfs:label "Genome type" ;
sld:type xsd:string .
cwl:in , , , , , ;
cwl:out , , , ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self.basename + \".tbi\")" .
rdfs:comment "MACS2 effective genome sizes: hs, mm, ce, dm or number, for example 2.7e9" ;
rdfs:label "Effective genome size" ;
sld:type xsd:string .
rdfs:comment "int: length (bases) of the SA pre-indexing string. Typically between 10 and\n15. Longer strings will use much more memory, but allow faster searches.\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--genomeSAindexNbases"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--genomeSAindexNbases"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "Ribosomal DNA file (*.fasta, *.fa). Default: hg19" ;
rdfs:label "Ribosomal DNA file (*.fasta, *.fa)" ;
cwl:format ;
sld:type cwl:File , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "# of chars consumed in initial lookup (default: 10)\n" ;
cwl:inputBinding [ CommandLineBinding:position 14 ;
CommandLineBinding:prefix "--ftabchars"
] ;
cwl:inputBinding [ CommandLineBinding:position 14 ;
CommandLineBinding:prefix "--ftabchars"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "Reference genome file (*.2bit, *.fasta, *.fa, *.fa.gz, *.fasta.gz). All chromosomes are included" ;
rdfs:label "Reference genome file (*.2bit, *.fasta, *.fa, *.fa.gz, *.fasta.gz)" ;
cwl:format ;
sld:type cwl:File .
rdfs:comment "If set, expect fields to be tab separated, normally expects white space separator\n" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-tab"
] ;
sld:type xsd:boolean , sld:null .
cwl:source ;
cwl:valueFrom "$(self + \"_star_genome\")" .
rdfs:comment "STAR generated mitochondrial DNA indices folder" ;
rdfs:label "STAR mitochondrial DNA indices" ;
cwl:outputSource ;
sld:type cwl:Directory .
rdfs:comment "Maximum available RAM (bytes) for genome generation. Default 31000000000" ;
rdfs:label "Limit maximum available RAM (bytes) for reference genome indices generation" ;
sld:type xsd:long , sld:null ;
ns2:layout [] .
a cwl:CommandLineTool ;
rdfs:comment "Tool returns directory with indices generated by STAR. If genome_dir input is not provided,\nuse default output directory name star_indices.\nOutput chr_name_length should not be moved outside the indices folder.\n" ;
ns3:original_cwlVersion "v1.2" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
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: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:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/star-genomegenerate.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
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:mainEntity ;
ns1:name "star-genomegenerate" ;
cwl:baseCommand ( "STAR" "--runMode" "genomeGenerate" ) ;
cwl:baseCommand ( "STAR" "--runMode" "genomeGenerate" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/star:v2.5.3a"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/star:v2.5.3a"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n return [\n {\n \"class\": \"Directory\",\n \"basename\": inputs.genome_dir,\n \"listing\": [],\n \"writable\": true}\n ]\n}\n"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n return [\n {\n \"class\": \"Directory\",\n \"basename\": inputs.genome_dir,\n \"listing\": [],\n \"writable\": true}\n ]\n}\n"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "star_build_stderr.log" ;
cwl:stdout "star_build_stdout.log" .
cwl:source ;
cwl:valueFrom "$(self + \"_bowtie_ribosomal\")" .
rdfs:comment "STAR generated stdout log for mitochondrial DNA indices" ;
rdfs:label "STAR stdout log for mitochondrial DNA indices" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:label "Genome details" ;
sld:type xsd:string , sld:null ;
ns2:preview [ CommandLineBinding:position
3 ] .
cwl:source .
cwl:source .
rdfs:comment "Bowtie generated ribosomal DNA indices folder" ;
rdfs:label "Bowtie ribosomal DNA indices" ;
cwl:outputSource ;
sld:type cwl:Directory .
cwl:source .
rdfs:comment "convert Ns in reference to As\n" ;
cwl:inputBinding [ CommandLineBinding:position 15 ;
CommandLineBinding:prefix "--ntoa"
] ;
cwl:inputBinding [ CommandLineBinding:position 15 ;
CommandLineBinding:prefix "--ntoa"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "If set, do not use compression\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-unc"
] ;
sld:type xsd:boolean , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Tool sorts data from `unsorted_file` by key\n\n`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.\n" ;
ns3:original_cwlVersion "v1.0" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
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:Andrey.Kartashov@cchmc.org" ;
ns1:name "Andrey Kartashov" ;
ns1:sameAs
] ;
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:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/linux-sort.cwl" ;
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 "linux-sort" ;
cwl:baseCommand ( "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.2"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"var get_output_filename = function() { if (inputs.output_filename) { return inputs.output_filename; } return inputs.unsorted_file.location.split('/').slice(-1)[0]; };"
] ;
cwl:stdout "$(get_output_filename())" .
rdfs:comment "Output filename\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename();\n } else {\n return self;\n }\n}\n"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "string: path to the GTF file with annotations\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbGTFfile"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--sjdbGTFfile"
] ;
sld:type cwl:File , sld:null .
rdfs:comment "Filter chromosomes while extracting FASTA from 2bit" ;
rdfs:label "Chromosome list to be included into the reference genome FASTA file" ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default "bed4+8" .
rdfs:comment "Bash function to run twoBitToFa or gunzip to extract and samtools to filter chromosomes\n" ;
cwl:default "#!/bin/bash\nset -e\nif [[ $0 == *.fasta ]] || [[ $0 == *.fa ]]; then\n echo \"Skip extract step\"\nelif [[ $0 == *.gz ]]; then\n gunzip -c $0 > \"${0%%.*}\".fa\n rm $0\nelse\n twoBitToFa $0 \"${0%%.*}\".fa\n rm $0\nfi\nif [ \"$#\" -ge 1 ]; then\n FILTER=${@:1}\n FILTER=$( IFS=$','; echo \"${FILTER[*]}\" )\n FILTER=(${FILTER//, / })\n echo \"Filtering by\" ${FILTER[*]}\n samtools faidx \"${0%%.*}\".fa ${FILTER[*]} > t.fa\n mv t.fa \"${0%%.*}\".fa\n rm \"${0%%.*}\".fa.fai\nfi\n" ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:string , sld:null .
a ns1:ScholarlyArticle ;
ns1:name "(Li, 2011) Improving SNP discovery by base alignment quality. Bioinformatics." ;
ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/21320865" .
rdfs:comment "1\nint: number of threads to run STAR\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--runThreadN"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--runThreadN"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "max bucket sz for blockwise suffix-array builder\n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--bmax"
] ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--bmax"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "int>0: suffux array sparsity, i.e. distance between indices: use bigger\nnumbers to decrease needed RAM at the cost of mapping speed reduction\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--genomeSAsparseD"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--genomeSAsparseD"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "MACS2 effective genome sizes: hs, mm, ce, dm or number, for example 2.7e9" ;
rdfs:label "Effective genome size" ;
cwl:outputSource ;
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type cwl:File .
a ns1:ScholarlyArticle ;
ns1:name "(Li et al., 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics." ;
ns1:url "http://www.ncbi.nlm.nih.gov/pubmed/19505943" .
a ns1:SoftwareSourceCode ;
ns1:about "Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.\nSTAR has a potential for accurately aligning long (several kilobases) reads that\nare emerging from the third-generation sequencing technologies\n" ;
ns1:codeRepository "https://github.com/alexdobin/STAR" ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "main author" ;
ns1:name "Alexander Dobin"
] ;
ns1:name "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"
] ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "main author" ;
ns1:name "Alexander Dobin"
] ;
ns1:name "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"
] ;
ns1:discussionUrl "https://github.com/alexdobin/STAR/issues" ;
ns1:license "https://opensource.org/licenses/GPL-3.0" ;
ns1:name "STAR" ;
ns1:programmingLanguage "C++" ;
ns1:targetProduct [ a ns1:SoftwareApplication ;
ns1:applicationCategory "command line tool" ;
ns1:softwareVersion "v2.5.3a"
] ;
ns1:targetProduct [ a ns1:SoftwareApplication ;
ns1:applicationCategory "command line tool" ;
ns1:softwareVersion "v2.5.3a"
] ;
ns1:url "https://github.com/alexdobin/STAR" .
rdfs:comment "Bowtie generated genome indices folder" ;
rdfs:label "Bowtie genome indices" ;
cwl:outputSource ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "-c" ) ;
cwl:baseCommand ( "bash" "-c" ) ;
cwl:cwlVersion cwl:v1.0 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/ucscuserapps:v358"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/ucscuserapps:v358"
] ;
cwl:inputs , , , ;
cwl:outputs , .
cwl:in , , , , , , , ;
cwl:out , , , ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self + \"_star_mitochondrial\")" .
rdfs:comment "STAR generated stderr log for mitochondrial DNA indices" ;
rdfs:label "STAR stderr log for mitochondrial DNA indices" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Genome chromosome length file" ;
rdfs:label "Genome chromosome length file" ;
cwl:format ;
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "If you are using a genome with a large (>5,000) number of references (chrosomes/scaffolds), you may need to reduce the\n--genomeChrBinNbits to reduce RAM consumption. For a genome with large number of contigs, it is recommended to scale\nthis parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).\ndefault: 18\n" ;
rdfs:label "Number of bins allocated for each chromosome of reference genome" ;
sld:type xsd:int , sld:null ;
ns2:layout [] .
rdfs:comment "Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory,\nbut allow faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled down to\nmin(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome,\nthis is equal to 7.\ndefault: 14\n" ;
rdfs:label "Length of SA pre-indexing string for reference genome indices" ;
sld:type xsd:int , sld:null ;
ns2:layout [] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.genome_dir + \"/chrNameLength.txt\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.genome_dir + \"/chrNameLength.txt\")" ] ;
sld:type cwl:File .
rdfs:comment "disable diff-cover (algorithm becomes quadratic)\n" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--nodc"
] ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--nodc"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Genome FASTA file" ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out , ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"refgene.gtf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"refgene.gtf" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Tool runs bowtie-build\nNot supported parameters:\n -c - reference sequences given on cmd line (as )\n" ;
ns3:original_cwlVersion "v1.2" ;
ns1:about "Usage: bowtie-build [options]* \n reference_in comma-separated list of files with ref sequences\n ebwt_outfile_base write Ebwt data to files with this dir/basename\nOptions:\n -f reference files are Fasta (default)\n -c reference sequences given on cmd line (as )\n --large-index force generated index to be 'large', even if ref\n has fewer than 4 billion nucleotides\n -C/--color build a colorspace index\n -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting\n -p/--packed use packed strings internally; slower, uses less mem\n --bmax max bucket sz for blockwise suffix-array builder\n --bmaxdivn max bucket sz as divisor of ref len (default: 4)\n --dcv diff-cover period for blockwise (default: 1024)\n --nodc disable diff-cover (algorithm becomes quadratic)\n -r/--noref don't build .3/.4.ebwt (packed reference) portion\n -3/--justref just build .3/.4.ebwt (packed reference) portion\n -o/--offrate SA is sampled every 2^offRate BWT chars (default: 5)\n -t/--ftabchars # of chars consumed in initial lookup (default: 10)\n --ntoa convert Ns in reference to As\n --seed seed for random number generator\n -q/--quiet verbose output (for debugging)\n -h/--help print detailed description of tool and its options\n --usage print this usage message\n --version print version information and quit\n" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
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: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:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/bowtie-build.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
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:mainEntity ;
ns1:name "bowtie-build" ;
cwl:baseCommand ( "bowtie-build" ) ;
cwl:baseCommand ( "bowtie-build" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/bowtie:v1.2.0"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/bowtie:v1.2.0"
] ;
cwl:inputs , , , , , , , , , , , , , , , , ;
cwl:outputs , ,