@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix SecondaryFileSchema: .
@prefix NetworkAccess: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var filename = inputs.unsorted_alignments.nameroot + \"_sorted.\";\n if (inputs.force_format !== undefined) {\n return filename + inputs.force_format.toLowerCase();\n }\n return filename + (inputs.unsorted_alignments.format == \"http://edamontology.org/format_2572\" ? \"bam\" : \"sam\");\n }\n" ] ;
sld:type cwl:File .
rdfs:comment "If true, use the file name to automatically assign the read groups value." ;
rdfs:label "Auto-assign read groups" ;
sld:default false ;
sld:type xsd:boolean .
rdfs:comment "aligned reads to be checked in sam or bam format" ;
cwl:format , ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".amb" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".ann" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".bwt.2bit.64" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".pac" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".0123" ] ;
sld:type cwl:File .
rdfs:label "Index the reference genome, if it isn't already indexed" ;
cwl:in ;
cwl:out ;
cwl:run ;
cwl:when "$(inputs.sequences.secondaryFiles !== undefined)\n" .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.bam" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.1" ;
cwl:arguments ( "$(inputs.sequences)" ) ;
cwl:baseCommand ( "bwa-mem2" "index" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "bwa-mem2" ;
SoftwarePackage:specs ;
SoftwarePackage:version "2.2.1"
]
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.sequences)" ]
] .
cwl:source .
cwl:in , , ;
cwl:out ;
cwl:run ;
cwl:when "$(inputs.do_auto_name !== null || inputs.details !== null)" .
rdfs:comment "This value must be unique among multiple samples in your experiment" ;
rdfs:label "Read group identifier (ID)" ;
sld:type xsd:string .
sld:type cwl:File , sld:null .
cwl:source .
a cwl:Workflow ;
rdfs:label "map medium and long reads (> 100 bp) against reference genome\n" ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
rdfs:label "Specify read group details manually." ;
sld:type , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Sort a bam file by read names." ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:prefix "--threads" ;
cwl:valueFrom "$(runtime.cores)"
]
[ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-m" ;
cwl:valueFrom "${ return(parseInt(runtime.ram/runtime.cores-100).toString() + \"M\") }"
]
[ CommandLineBinding:prefix "-T" ;
cwl:valueFrom "$(runtime.tmpdir)"
]
"--no-PG"
) ;
cwl:baseCommand ( "samtools" "sort" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 15000
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.14--hb421002_0"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "samtools" ;
SoftwarePackage:specs ;
SoftwarePackage:version "1.14"
]
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "${\n var filename = inputs.unsorted_alignments.nameroot + \"_sorted.\";\n if (inputs.force_format !== undefined) {\n return filename + inputs.force_format.toLowerCase();\n }\n return filename + (inputs.unsorted_alignments.format == \"http://edamontology.org/format_2572\" ? \"bam\" : \"sam\");\n }\n" .
cwl:source .
cwl:source .
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "reads to be checked in sam format" ;
cwl:format ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
rdfs:comment "* coordinate: Sort by chromosomal coordinates\n* name: Sort by read names (i.e., the QNAME field)\n* unsorted: Not sorted (sorted as input)\n" ;
rdfs:label "How to sort the alignments, if at all" ;
sld:default "coordinate" ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self === \"name\" ? true : false)" .
rdfs:label "Library name (LB)" ;
sld:type xsd:string .
rdfs:comment "If true, will force binary output (BAM)" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type sld:null ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.0" ;
ExpressionTool:expression "${\n var rg_auto_name = read_group_name_default(inputs.input1, inputs.input2);\n var rg_id = rg_auto_name;\n var rg_string = \"\";\n if (inputs.details) {\n rg_string = \"@RG\\\\tID:\" + inputs.details.identifier;\n rg_string += \"\\\\tPL:\" + inputs.details.platform;\n rg_string += \"\\\\tLB:\" + inputs.details.library;\n } else {\n rg_string = \"@RG\\\\tID:\" + rg_id;\n }\n return {\"read_group_name\": rg_string};\n }\n" ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"function clean(name) {\n return name.replace(/[^\\w\\-_\\.]/, '_');\n};\nfunction read_group_name_default(input1, input2) {\n // input1: File\n // input2: File?\n var input_name1 = clean(input1.nameroot);\n if (input2 === null) {\n return input_name1;\n }\n var input_name2 = clean(input2.nameroot);\n var common_prefix = \"\";\n for (var index = 0; index < input_name1.length; index++) {\n if (input_name1.charAt(index) == input_name2.charAt(index)) {\n common_prefix += input_name1.charAt(index);\n }\n }\n if (common_prefix.length > 3) {\n return common_prefix;\n }\n return input_name1;\n};\n"
] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
sld:type xsd:string .
rdfs:label "Alignments of the reads to the references genome" ;
cwl:format ;
cwl:outputSource , ;
cwl:pickValue "the_only_non_null" ;
sld:type cwl:File .
rdfs:label "Second (reverse) set of reads (if using paired reads)." ;
cwl:format , ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type cwl:File , sld:null .
sld:type , sld:null .
rdfs:comment "If true, will sort by name, otherwise will sort by genomic position" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-n"
] ;
sld:default false ;
sld:type xsd:boolean .
rdfs:label "If not sorting the reads; convert textual alignments (SAM) to binary (BAM) format" ;
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:when "$(inputs.sort_mode === \"unsorted\")" .
rdfs:label "Sort the reads, if requested" ;
cwl:in , , , ;
cwl:out ;
cwl:run ;
cwl:when "$(inputs.sort_mode !== \"unsorted\")" .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.sam" ] ;
sld:type cwl:File .
sld:fields , , ;
sld:type sld:record .
rdfs:label "Sequences to map to the reference genome." ;
cwl:format , ;
sld:type cwl:File .
rdfs:comment "read group header line such as '@RG\\tID:foo\\tSM:bar'\n" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-R" ] ;
sld:type xsd:string , sld:null .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Convert SAM to BAM.\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "-h"
]
[ CommandLineBinding:position 1 ;
cwl:valueFrom "-b"
]
"--no-PG"
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.14--hb421002_0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 10000
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "samtools" ;
SoftwarePackage:specs ;
SoftwarePackage:version "1.14"
]
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:stdout "$(inputs.sam.nameroot).bam" .
cwl:source .
cwl:source .
cwl:source .
cwl:format ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "map medium and long reads (> 100 bp) against reference genome\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-t" "$(runtime.cores)" "-v" "1" ) ;
cwl:baseCommand ( "bwa-mem2" "mem" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "bwa-mem2" ;
SoftwarePackage:specs ;
SoftwarePackage:version "2.2.1"
]
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "${\n var filename = inputs.reads.nameroot;\n if (inputs.paired_reads_2) {\n filename += \"_\" + inputs.paired_reads_2.nameroot;\n }\n return filename += \".sam\"\n }\n" .
sld:default "BAM" .
rdfs:label "Platform/technology used to produce the reads (PL)" ;
sld:type [ sld:symbols , , , , , , ;
sld:type sld:enum
] ;
sld:type [ sld:symbols , , , , , , ;
sld:type sld:enum
] .
cwl:source .
rdfs:label "Reference genome sequences, optionally already indexed for BWA-Mem2." ;
cwl:format ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".ann" ;
SecondaryFileSchema:required false
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".0123" ;
SecondaryFileSchema:required false
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".amb" ;
SecondaryFileSchema:required false
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".bwt.2bit.64" ;
SecondaryFileSchema:required false
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".pac" ;
SecondaryFileSchema:required false
] ;
sld:type cwl:File .
cwl:pickValue "first_non_null" ;
cwl:source , .
cwl:format ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sequences.basename)" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".amb" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".0123" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".bwt.2bit.64" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".pac" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
".ann" ] ;
sld:type cwl:File .
rdfs:label "First (forward) set of reads (or unpaired reads)." ;
cwl:format , ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .