@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:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-window_size"
] ;
sld:type xsd:int , sld:null .
rdfs:label "Collect BlastDB" ;
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-taxid_map"
] ;
sld:type cwl:File , sld:null .
cwl:default "6 qseqid sseqid pident slen length mismatch gapopen qlen qstart qend sstart send evalue bitscore score staxid" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-outfmt"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default true .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-gapopen"
] ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "NCBI BlastN Nucleotide-Nucleotide BLAST" ;
rdfs:label "BlastN" ;
ns2:original_cwlVersion "v1.0" ;
ns1:author [ a ns1:Person ;
ns1:email "mailto:r78v10a07@gmail.com" ;
ns1:identifier "https://orcid.org/0000-0002-4108-5982" ;
ns1:name "Roberto Vera Alvarez"
] ;
cwl:baseCommand ( "blastn" ) ;
cwl:cwlVersion ;
cwl:hints , ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "${\n return inputs.num_threads ? inputs.num_threads : 1\n }\n"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "blast" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/blast" ;
SoftwarePackage:version "2.12.0"
] ;
SoftwareRequirement:packages [ SoftwarePackage:package "blast" ;
SoftwarePackage:specs "https://anaconda.org/bioconda/blast" ;
SoftwarePackage:version "2.12.0"
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-min_raw_gapped_score"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-subject"
] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-gi_mask"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-mask_data"
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.out)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-import_search_strategy"
] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:label "Create FASTA from FASTQ" ;
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "Create FASTA from FASTQ" ;
ns2:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "zcat" ) ;
cwl:baseCommand ( "zcat" ) ;
cwl:cwlVersion ;
cwl:hints ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "$(inputs.fastq1.nameroot + \".fsa\")" .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-negative_taxids"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "in=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
cwl:default "myblastdb" .
rdfs:label "Creates clean FASTQ" ;
cwl:in , , , , , ;
cwl:out , ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-gilist"
] ;
sld:type xsd:string , sld:null .
cwl:valueFrom "${\n if (inputs.in2 != null){\n var nameroot = inputs.in2.nameroot;\n if (nameroot.endsWith(\".fastq\")){\n nameroot = nameroot.replace(\".fastq\", \"\");\n }else if (nameroot.endsWith(\".fq\")){\n nameroot = nameroot.replace(\".fq\", \"\");\n }\n if (nameroot.endsWith(\"_2\")){\n nameroot = nameroot.replace('_2', '_clean_2.fastq.gz');\n }else if (nameroot.includes(\"_R2_\")){\n nameroot = nameroot.substring(1, nameroot.indexOf(\"_R2_\")) + '_clean_2.fastq.gz';\n }\n return nameroot;\n }\n return null;\n}\n" .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-strand"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-culling_limit"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-best_hit_overhang"
] ;
sld:type xsd:float , sld:null .
a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:24.04" .
Parameter:streamable true ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fastq1.nameroot + \".fsa\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fastq1.nameroot + \".fsa\")" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-entrez_query"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-xdrop_gap_final"
] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-num_threads"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-export_search_strategy"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-searchsp"
] ;
sld:type xsd:long , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-evalue"
] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-xdrop_gap"
] ;
sld:type xsd:float , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.out).*" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-best_hit_score_edge"
] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-hash_index"
] ;
sld:type xsd:boolean , sld:null .
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-out"
] ;
sld:type xsd:string .
cwl:valueFrom "${ return inputs.query.nameroot + \".tsv\";}" .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-reward"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-db_hard_mask"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "in2=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-subject_loc"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-query_loc"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-taxids"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-blastdb_version"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-title"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-subject_besthit"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-taxidlist"
] ;
sld:type cwl:File , sld:null .
a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0" .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-db" ;
cwl:valueFrom "${ return inputs.dbdir.path + \"/\" + self;}"
] ;
sld:type xsd:string .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-xdrop_ungap"
] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-max_target_seqs"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-mt_mode"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-remote"
] ;
sld:type xsd:boolean , sld:null .
cwl:default 5 .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-index_name"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-parse_deflines"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "out2=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-logfile"
] ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Extract read IDs" ;
cwl:baseCommand ( "cat" ) ;
cwl:baseCommand ( "cat" ) ;
cwl:hints ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "$(inputs.tsv.nameroot + \"_unique.ids\")" .
cwl:default "6 qseqid saccver qstart qend length evalue bitscore score" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.out2)" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "out=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-query"
] ;
sld:type cwl:File .
cwl:default 1750000000000 .
sld:type xsd:string .
cwl:default "myblastdb" .
cwl:default "'{print $1}'" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "awk" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "awk" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
sld:type cwl:File .
cwl:default "true" .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-off_diagonal_range"
] ;
sld:type xsd:int , sld:null .
rdfs:label "Create FASTA from FASTQ" ;
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-num_descriptions"
] ;
sld:type xsd:int , sld:null .
cwl:default "nucl" .
cwl:outputSource ;
sld:type cwl:File .
a cwl:ExpressionTool ;
rdfs:comment "Group all input files in a directory" ;
rdfs:label "files2dir" ;
ns2:original_cwlVersion "v1.2" ;
ExpressionTool:expression "${\n var listing = [];\n for (var i = 0; i < inputs.files.length; i++) {\n listing.push(inputs.files[i]);\n }\n return {\n \"output\": {\n \"class\": \"Directory\",\n \"basename\": inputs.dir,\n \"listing\": listing\n }\n };\n}\n" ;
cwl:cwlVersion ;
cwl:hints ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-line_length"
] ;
sld:type xsd:int , sld:null .
a cwl:Workflow ;
rdfs:comment "This workflow clean up vectros from fastq files" ;
rdfs:label "FASTQ Vector Removal" ;
ns2: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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-sorthits"
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-parse_seqids"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:default "|" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
Parameter:streamable true ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.export_search_strategy)" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-negative_seqidlist"
] ;
sld:type xsd:string , sld:null .
cwl:default 700 .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-window_masker_db"
] ;
sld:type xsd:string , sld:null .
cwl:default "yes" .
cwl:default 1 .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-dust"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-db_soft_mask"
] ;
sld:type xsd:string , sld:null .
cwl:default "f" .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "include=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
Parameter:streamable true ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tsv.nameroot + \"_unique.ids\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tsv.nameroot + \"_unique.ids\")" ] ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-use_index"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-taxid"
] ;
sld:type xsd:int , sld:null .