@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix dct: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix CommandLineTool: .
@prefix ExpressionTool: .
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "filename to split" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--fastq1" ] ;
sld:type cwl:File .
cwl:source .
cwl:valueFrom "${ return inputs.project_prefix + \"_GcBiasMetrics.txt\"; }" .
rdfs:comment "Absolute Copy Number Data, as defined by Absolute, to use in power calculations" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--absolute_copy_number_data"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Convert a Picard interval list file to a UCSC BED format\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python" "/usr/bin/list2bed.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 3 ;
ResourceRequirement:ramMin 2000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-list2bed:1.0.1"
] .
cwl:source .
rdfs:comment "Enable GATK threading efficiency monitoring" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--monitorThreadEfficiency"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string .
cwl:source .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING| SET_Q_ZERO|SET_Q_ZERO_BASE_N| REMOVE_REF_BIAS)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--solid_recal_mode"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Matched_Norm_Sample_Barcode to report in the MAF" ;
cwl:default "NORMAL" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--normal-id" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Indicate to move indels to 3-prime if alternative alignment can be achieved." ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-3"
] ;
sld:type xsd:boolean , sld:null .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:in , , , , , , , ;
cwl:out , , , , , , , , , ;
cwl:run .
rdfs:comment "lines which should be appended to the VCF header" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--header-lines" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
sld:type xsd:string .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Rename sample IDs on-the-fly at runtime using the provided mapping file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sample_rename_mapping_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:valueFrom "${ return \"all_reads_hsmerics_dump.txt\"; }" .
rdfs:comment "Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically. Default value - null." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "PROGRAM_GROUP_COMMAND_LINE=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "VALIDATION_STRINGENCY=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Compression level to use for writing BAM files (0 - 9, higher is more compressed)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bam_compression"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Remove snps/indels from the output maf where a complex variant is called\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python" "/usr/bin/remove_variants.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-remove-variants:0.1.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 3 ;
ResourceRequirement:ramMin 8000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
rdfs:comment "The total number of BAM file handles to keep open simultaneously" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--num_bam_file_handles"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "write out tumor read depth in WIGGLE format to this file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tumor_depth_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string .
rdfs:comment "Reduce memory usage in multi-threaded code at the expense of threading efficiency" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--lowMemoryMode"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment " Write output to a file [standard output]" ;
cwl:default "bcftools_concat.vcf" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output" ] ;
sld:type xsd:string .
sld:type xsd:string .
rdfs:comment "Parameter to pass to the VCF/BCF IndexCreator" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant_index_parameter"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:in ;
cwl:out , , , , , , , , , , , , , , ;
cwl:run .
rdfs:comment "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--interval_padding"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default "1" .
cwl:source .
rdfs:comment "The format of the output file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--outputFormat"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-V"
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-V"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Tumor total depth threshold" ;
cwl:default 5 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--totaldepth" ] ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type [ sld:items [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type sld:array
] .
rdfs:comment "This option performs length trimming of quality/adapter/RRBS trimmed reads for paired-end files. To pass the validation test, both sequences of a sequence pair are required to have a certain minimum length which is governed by the option --length (see above). If only one read passes this length threshold the other read can be rescued (see option --retain_unpaired). Using this option lets you discard too short read pairs without disturbing the sequence-by-sequence order of FastQ files which is required by many aligners. Trim Galore! expects paired-end files to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz ... ." ;
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"--paired" ] ;
sld:type xsd:boolean , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
CommandLineTool:stdin "$(inputs.input_vcf.path)" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-N" ;
cwl:valueFrom "${\n return inputs.N + \"|\" + inputs.N2;\n}"
]
) ;
cwl:baseCommand ( "perl" "/usr/bin/vardict/var2vcf_paired.pl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 6 ;
ResourceRequirement:ramMin 32000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-vardict:1.5.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "${ return inputs.vcf; }" .
rdfs:comment "reference sequence FASTA FILE [null]\n" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-T"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-T"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-T"
] ;
sld:type cwl:File , sld:null .
cwl:valueFrom "${ return inputs.normal.ID; }" .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-R" ;
cwl:valueFrom "@RG\\\\tID:$(inputs.lane_id)\\\\tSM:$(inputs.sample_id)\\\\tLB:$(inputs.sample_id)\\\\tPL:Illumina\\\\tPU:$(inputs.lane_id)"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-t" ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-R" ;
cwl:valueFrom "@RG\\\\tID:$(inputs.lane_id)\\\\tSM:$(inputs.sample_id)\\\\tLB:$(inputs.sample_id)\\\\tPL:Illumina\\\\tPU:$(inputs.lane_id)"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-t" ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "bwa" "mem" ) ;
cwl:baseCommand ( "bwa" "mem" ) ;
cwl:cwlVersion ;
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:ResourceRequirement ;
ResourceRequirement:coresMin 6 ;
ResourceRequirement:ramMin 32000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 6 ;
ResourceRequirement:ramMin 32000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/bwa_mem:0.7.12"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/bwa_mem:0.7.12"
] ;
cwl:stdout "$(inputs.reads[0].basename.replace('fastq.gz', 'sam'))" .
rdfs:comment "Stop execution cleanly as soon as maxRuntime has been reached" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--maxRuntime"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:valueFrom "${ return inputs.normal.ID; }" .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.output_directory_name + \"/\" + inputs.output_prefix + \"_concordance*.pdf\")\n return inputs.output_directory_name + \"/\" + inputs.output_prefix + \"_concordance*.pdf\";\n return null;\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.output_directory_name + \"/\" + inputs.output_prefix + \"_concordance*.pdf\")\n return inputs.output_directory_name + \"/\" + inputs.output_prefix + \"_concordance*.pdf\";\n return null;\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:source .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string , sld:null .
sld:type [ sld:fields , , , , , , , , , , , , , ;
sld:type sld:record
] ;
sld:type [ sld:fields , , , , , , , , , , , , , ;
sld:type sld:record
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "MAX_RECORDS_IN_RAM=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:valueFrom "${ return [\"BadCigar\"];}" .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Show detailed messages." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--verbose" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Set mapq for alignments that map equally well to reference and an ABRA generated contig. default of -1 disables (default - -1)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--amq"
] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .