@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:source .
rdfs:comment "BAM alignment file" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"*_1.fastq*" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Download .sra format sequence data from NCBI Sequence Read Archive" ;
rdfs:label "download_sra" ;
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "directory containing FastA file and index for BWA aligner" ;
sld:type cwl:Directory .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "samtools-sam2bam-1.9--h8ee4bcc_1" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments () ;
cwl:baseCommand ( "samtools" "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.9--h8ee4bcc_1"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "output.sort.bam" .
cwl:outputBinding [ CommandOutputBinding:glob
"*_fastqc.html" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*_fastqc.html" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*_fastqc.html" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*_fastqc.html" ] ;
sld:type cwl:File .
rdfs:comment "SAM alignment file" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-t" ] ;
sld:type xsd:int .
cwl:source .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"output.sort.bam" ] ;
sld:type cwl:File .
rdfs:comment "FastQ file from next-generation sequencers" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"*fastq*" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Mapping onto a reference genome" ;
rdfs:label "map" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"*_2.fastq*" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Quality control for fastq file (fq2) before trimming" ;
rdfs:label "qc2" ;
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "Convert SAM to BAM" ;
rdfs:label "sam2bam" ;
cwl:in ;
cwl:out ;
cwl:run .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq2.basename).trim.2U.fastq" ] ;
sld:type cwl:File .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--readids" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "name of reference (e.g., hs37d5)" ;
sld:type xsd:string .
rdfs:comment "Sort BAM" ;
rdfs:label "sort" ;
cwl:in ;
cwl:out ;
cwl:run .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq2.basename).trim.2P.fastq" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--split-files" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Quality control for fastq file (fq2) after trimming" ;
rdfs:label "qc2P" ;
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "bwa-mem-PE-0.7.15--1" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-t" ;
cwl:valueFrom "4"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-K" ;
cwl:valueFrom "100000000"
]
[ CommandLineBinding:position 3 ;
cwl:valueFrom "-Y"
]
[ CommandLineBinding:position 4 ;
cwl:valueFrom "-p"
]
[ CommandLineBinding:position 5 ;
cwl:valueFrom "$(inputs.fadir.path)/$(inputs.ref).fa"
]
) ;
cwl:baseCommand ( "bwa" "mem" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bwa:0.7.15--1"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "output.sam" .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq1.basename).trim.1U.fastq" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "adaptor trimming" ;
rdfs:label "trimPE" ;
cwl:in , ;
cwl:out , ;
cwl:run .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq1.basename).trim.1P.fastq" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*sra" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "FastQ file from next-generation sequencers" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type cwl:File .
rdfs:comment "Quality control for fastq file (fq1) after trimming" ;
rdfs:label "qc1P" ;
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "The number of cores to be used for parallel exec of fastq-dump" ;
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:position
50 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "FastQ file from next-generation sequencers" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:label "test-workflow" ;
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:outputSource ;
sld:type cwl:File .
cwl:source .
rdfs:comment "name of reference (e.g., hs37d5) for BWA aligner" ;
sld:type xsd:string .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gzip" ] ;
sld:type xsd:boolean , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "A simple download tool to get .sra file from a repository of INSDC members. https://github.com/inutano/download-sra" ;
rdfs:label "download-sra: A simple download tool to get .sra file" ;
ns1:original_cwlVersion "v1.0" ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/inutano/download-sra:0.1.2"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs .
cwl:outputSource ;
sld:type cwl:File .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"output.bam" ] ;
sld:type cwl:File .
rdfs:comment "FastQ file from next-generation sequencers" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "samtools-sam2bam-1.9--h8ee4bcc_1" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments () ;
cwl:baseCommand ( "samtools" "view" "-bS" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.9--h8ee4bcc_1"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "output.bam" .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--split-spot" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "directory containing FastA file and index" ;
sld:type cwl:Directory .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"output.sam" ] ;
sld:type cwl:File .
rdfs:comment "A list of SRA Run ID such as ERR034597" ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "fastqc" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "."
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "."
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "."
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "."
]
) ;
cwl:baseCommand ( "fastqc" ) ;
cwl:baseCommand ( "fastqc" ) ;
cwl:baseCommand ( "fastqc" ) ;
cwl:baseCommand ( "fastqc" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
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 "quay.io/biocontainers/fastqc:0.11.7--pl5.22.0_2"
] ;
cwl:inputs ;
cwl:outputs .
a cwl:CommandLineTool ;
rdfs:label "trimmomatic-0.38" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "/usr/local/share/trimmomatic/trimmomatic.jar"
]
[ CommandLineBinding:position 2 ;
cwl:valueFrom "PE"
]
[ CommandLineBinding:position 5 ;
cwl:valueFrom "$(inputs.fq1.basename).trim.1P.fastq"
]
[ CommandLineBinding:position 6 ;
cwl:valueFrom "$(inputs.fq1.basename).trim.1U.fastq"
]
[ CommandLineBinding:position 7 ;
cwl:valueFrom "$(inputs.fq2.basename).trim.2P.fastq"
]
[ CommandLineBinding:position 8 ;
cwl:valueFrom "$(inputs.fq2.basename).trim.2U.fastq"
]
[ CommandLineBinding:position 9 ;
cwl:valueFrom "ILLUMINACLIP:/usr/local/share/trimmomatic/adapters/TruSeq2-PE.fa:2:40:15"
]
) ;
cwl:baseCommand ( "java" "-jar" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/trimmomatic:0.38--1"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs , , , .
rdfs:comment "parallel execution of fastq-dump to convert .sra to .fastq.gz" ;
rdfs:label "pfastq-dump" ;
cwl:in , ;
cwl:out , ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:comment "pfastq-dump is a bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper. --stdout option is additionally supported, but almost same features. It also uses -N and -X options of fastq-dump to specify blocks of data to be decompressed separately. https://github.com/inutano/pfastq-dump" ;
rdfs:label "pfastq-dump: A bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "pfastq-dump" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/inutano/sra-toolkit:v2.9.2"
] ;
cwl:inputs , , , , , , ;
cwl:outputs , , .
cwl:default "ncbi" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-r"
] ;
sld:type xsd:string .
rdfs:comment "Quality control for fastq file (fq1) before trimming" ;
rdfs:label "qc1" ;
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "(optional) The repository from which the data was downloaded (ncbi/ebi/ddbj). Default value is NCBI." ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--skip-technical" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "FastQ file from next-generation sequencers" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
7 ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .