@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: .
a cwl:CommandLineTool ;
rdfs:comment "The program can handle the following classes of inputs:\n - single end reads (only reads File and rg string provided)\n - reads with mates (reads File, mates File, and rg string provided)\n - interleaved reads (reads File provided, rg string provided, and interleaved set to true)\nThis tool runs the following programs:\n - bwa mem | samblaster | sambamba view | sambamba sort" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "set -eo pipefail\nbwa mem -K 100000000 ${if (inputs.interleaved) {return '-p';} else {return \"\"}} -v 3 -t 36 -Y $(inputs.ref.path) -R '${return inputs.rg}' ${return inputs.reads.path} ${if (inputs.mates != null) {return inputs.mates.path} else {return \"\"}} | /opt/samblaster/samblaster -i /dev/stdin -o /dev/stdout | /opt/sambamba_0.6.3/sambamba_v0.6.3 view -t 36 -f bam -l 0 -S /dev/stdin | /opt/sambamba_0.6.3/sambamba_v0.6.3 sort -t 36 --natural-sort -m 15GiB --tmpdir ./ -o ${if (inputs.reads != null) {return inputs.reads.nameroot} else {return \"\"}}.unsorted.bam -l 5 /dev/stdin"
]
) ;
cwl:baseCommand ( "/bin/bash" "-c" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "zhangb1/bwa-kf-bundle:0.1.17"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 36 ;
ResourceRequirement:ramMin 50000
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.bam" ] ;
sld:type cwl:File .
rdfs:comment "Primary reads file" ;
sld:type cwl:File .
cwl:source .
cwl:hints [ a ] ;
cwl:in ;
cwl:out ;
cwl:run .
cwl:in , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
sld:type cwl:File .
rdfs:comment "Mates file for the reads" ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "Input fastq file" ;
sld:type cwl:File .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:source .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob "*.fq" ;
CommandOutputBinding:outputEval
"${\n if (self.length == 0) return [inputs.input_fastq]\n else return self\n}"
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:source .
rdfs:comment "Formatted RG header to use in the resulting BAM, check BWA for formatting guidelines (e.g. escaped tabs '\\t')" ;
sld:type xsd:string .
rdfs:comment "The reads input is interleaved" ;
cwl:default false ;
sld:type xsd:boolean .
rdfs:comment "Reference fasta file with associated indexes" ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "This tool will chomp any fastq larger than the max size (10 gb by default) into 320000000 line chunks (80M reads). \nPrograms used in this tool:\n - zcat | split\n - ls | mv" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "set -eo pipefail\n\nif [ $(inputs.input_fastq.size) -gt $(inputs.max_size) ]; then\n zcat $(inputs.input_fastq.path) | split -dl 320000000 - reads-\n ls reads-* | xargs -i mv {} {}.fq\nelse\n echo \"FASTQ not large enough to split.\"\nfi"
]
) ;
cwl:baseCommand ( "/bin/bash" "-c" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 8000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "kfdrc/bwa-bundle:dev"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
rdfs:comment "The maximum size (in bytes) that an input bam can be before the FASTQ is split" ;
cwl:default 10000000000 ;
sld:type xsd:int .