@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
rdfs:comment "Don't recalibrate bases with quality scores less than this threshold (with -BQSR)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--preserve_qscores_less_than"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Fraction of reads to downsample to" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsample_to_fraction"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Unit of time used by maxRuntime (NANOSECONDS|MICROSECONDS| MILLISECONDS|SECONDS|MINUTES| HOURS|DAYS)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--maxRuntimeUnits"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Emit the OQ tag with the original base qualities (with -BQSR)" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--emit_original_quals"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "I=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
rdfs:comment "Pedigree files for samples" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--pedigree"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Pedigree string for samples" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--pedigreeString"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "cmo-index" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "cmo_index" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 3 ;
ResourceRequirement:ramMin 16000
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.bam)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-cmo-utils:1.9.15"
] .
rdfs:comment "Ignore warnings about base quality score encoding" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--allow_potentially_misencoded_quality_scores"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Keep program records in the SAM header" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--keep_program_records"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Keep program records in the SAM header" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--keep_program_records"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING| SET_Q_ZERO|SET_Q_ZERO_BASE_N| REMOVE_REF_BIAS)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--solid_recal_mode"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Compression level to use for writing BAM files (0 - 9, higher is more compressed)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bam_compression"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:valueFrom "${ return [\"3\"];}" .
rdfs:comment "Input covariates table file for on-the-fly base quality score recalibration" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--BQSR"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Splice junctions definition file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--junctions"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Logging level (trace,debug,info,warn, error) (default - info)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--log"
] ;
sld:type xsd:string , sld:null .
cwl:in , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Just output sites without genotypes (i.e. only the first 8 columns of the VCF)" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sites_only"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "BAQ gap open penalty" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--baqGapOpenPenalty"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Compression level of output bam file (s) (default - 5)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--cl"
] ;
sld:type xsd:string , sld:null .
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
] .
rdfs:comment "Max reads to keep in memory per sample during the sort phase. When this value is exceeded, sort spills to disk (default - 1000000)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--msr"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Just output sites without genotypes (i.e. only the first 8 columns of the VCF)" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sites_only"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Sample name to be included in the analysis. Can be specified multiple times." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sample_name"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "default quality for the base mismatches covariate" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mismatches_default_quality"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.out)\n return inputs.out;\n return null;\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "Type of IndexCreator to use for VCF/BCF indices (DYNAMIC_SEEK| DYNAMIC_SIZE|LINEAR|INTERVAL)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant_index_type"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Maximum pre-pruned nodes in regional assembly (default - 150000)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--maxn"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "One or more genomic intervals over which to operate" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--intervals" ;
CommandLineBinding:separate true
] ;
sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "BED file containing target regions" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--targets"
] ;
sld:type cwl:File , xsd:string , sld:null .
rdfs:comment "How strict should we be with validation (STRICT|LENIENT| SILENT)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--validation_strictness"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Type of IndexCreator to use for VCF/BCF indices (DYNAMIC_SEEK| DYNAMIC_SIZE|LINEAR|INTERVAL)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant_index_type"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Use a non-deterministic random seed" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--nonDeterministicRandomSeed"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Reads arguments from the specified file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--arg_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:in , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
rdfs:comment "default quality for the base insertions covariate" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--insertions_default_quality"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
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 .
rdfs:comment "Fraction of reads to downsample to" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsample_to_fraction"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File .
rdfs:comment "Soft clip contig args [max_contigs, min_base_qual,frac_high_qual_bases, min_soft_clip_len] (default - 16,13,80,15)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sc"
] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "An output file created by the walker. Will overwrite contents if file exists" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--out"
] ;
sld:type xsd:string .
rdfs:comment "Remove program records from the SAM header" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--remove_program_records"
] ;
sld:type xsd:boolean , sld:null .
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
] .
rdfs:comment "Disable printing of base insertion and deletion tags (with -BQSR)" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--disable_indel_quals"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Enable unsafe operations - nothing will be checked at runtime (ALLOW_N_CIGAR_READS| ALLOW_UNINDEXED_BAM| ALLOW_UNSET_BAM_SORT_ORDER| NO_READ_ORDER_VERIFICATION| ALLOW_SEQ_DICT_INCOMPATIBILITY| LENIENT_VCF_PROCESSING|ALL)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--unsafe"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Type of read downsampling to employ at a given locus (NONE| ALL_READS|BY_SAMPLE)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsampling_type"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "refactor cigar string with NDN elements to one element" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--refactor_NDN_cigar_string"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Interval merging rule for abutting intervals (ALL| OVERLAPPING_ONLY)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--interval_merging"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Fraction of reads to downsample to" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsample_to_fraction"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "output bed file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output_file" ] ;
sld:type xsd:string .
cwl:outputSource ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:valueFrom "${ return [\"20\"];}" .
rdfs:comment "Filters to apply to reads before analysis" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--read_filter"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Assembly minimum contig length (default - -1)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mcl"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "output intervals that fail the coverage threshold instead" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--uncovered"
] ;
sld:type xsd:boolean , sld:null .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--filter_mismatching_base_and_quals"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Unit of time used by maxRuntime (NANOSECONDS|MICROSECONDS| MILLISECONDS|SECONDS|MINUTES| HOURS|DAYS)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--maxRuntimeUnits"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "Tag to identify this GATK run as part of a group of runs" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tag"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Do not use unmapped reads anchored by mate to trigger assembly. These reads are still eligible to contribute to assembly" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--sua"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Size of the k-mer context to be used for base mismatches" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mismatches_context_size"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--simplifyBAM"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "refactor cigar string with NDN elements to one element" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--refactor_NDN_cigar_string"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
cwl:baseCommand ( "cat" ) ;
cwl:baseCommand ( "cat" ) ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:stdout "$(inputs.output_filename)" .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.O)\n return inputs.O.concat('.insert_size_metrics');\n return null;\n}\n" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Type of read downsampling to employ at a given locus (NONE|ALL_READS|BY_SAMPLE)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsampling_type"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Run reporting mode (NO_ET|AWS| STDOUT)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--phone_home"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Interval merging rule for abutting intervals (ALL| OVERLAPPING_ONLY)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--interval_merging"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "One or more covariates to be used in the recalibration. Can be specified multiple times" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"--covariate" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--filter_bases_not_stored"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Reads arguments from the specified file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--arg_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "The minimum allowable base quality score to be counted for coverage" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--minBaseQuality"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Type of BAQ calculation to apply in the engine (OFF| CALCULATE_AS_NECESSARY| RECALCULATE)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--baq"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Min edge pruning ratio. Default value is appropriate for relatively sensitive somatic cases. May be increased for improved speed in germline only cases. (default - 0.01)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mer"
] ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "None\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-jar" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/usr/bin/abra.jar"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-Xms$(Math.round(parseInt(runtime.ram)/1910))G"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-Xmx$(Math.floor(parseInt(runtime.ram)/1048) - 1)G"
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tmpdir" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "$(runtime.tmpdir)"
]
) ;
cwl:baseCommand ( "java" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-abra:2.17"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 16 ;
ResourceRequirement:ramMin "$(inputs.abra_ram_min)"
] .
rdfs:comment "Number of CPU threads to allocate per data thread" ;
cwl:default "2" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--num_cpu_threads_per_data_thread"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Set the logging location" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--log_to_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Input file containing sequence data (SAM or BAM)" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"--input_file" ] ;
sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "VCF containing known (or suspected) variant sites. Very large files should be avoided." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--in-vcf"
] ;
sld:type xsd:string , sld:null .
sld:type [ sld:items [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type sld:array
] ;
sld:type [ sld:items [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type sld:array
] .
rdfs:comment "List of metrics programs to apply during the pass through the SAM file. Possible values - {CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list." ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type sld:null ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "PROGRAM=" ;
CommandLineBinding:separate false
] ;
sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "filter out reads with CIGAR containing the N operator, instead of stop processing and report an error." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--filter_reads_with_N_cigar"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "The active region extension; if not provided defaults to Walker annotated default" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--activeRegionExtension"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Enable threading efficiency monitoring" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--monitorThreadEfficiency"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Optional file to which assembled contigs are written" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--contigs"
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.O)\n return inputs.O.concat('.quality_by_cycle.pdf');\n return null;\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "Parameter to pass to the VCF/BCF IndexCreator" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant_index_parameter"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Set the minimum level of logging" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--logging_level"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Emit the OQ tag with the original base qualities (with -BQSR)" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--emit_original_quals"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Output the raw activity profile results in IGV format" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--activityProfileOut"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Compression level to use for writing BAM files (0 - 9, higher is more compressed)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bam_compression"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Max read move distance (default - 1000)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--dist"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "If true (default), then the sort order in the header file will be ignored. Default value - true. This option can be set to 'null' to clear the default value. Possible values - {true, false}" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "ASSUME_SORTED=True" ;
CommandLineBinding:separate false
] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.out)\n return inputs.out;\n return null;\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "number of distinct quality scores in the quantized output" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--quantizing_levels"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Type of read downsampling to employ at a given locus (NONE| ALL_READS|BY_SAMPLE)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--downsampling_type"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Always output all the records in VCF FORMAT fields, even if some are missing" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--never_trim_vcf_format_field"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Max assembled contigs (default - 64)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mac"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
rdfs:comment "GATK key file required to run with -et NO_ET" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--gatk_key"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Unset duplicate flag" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--undup"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "The minimum allowable coverage to be considered covered" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--coverage_threshold"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Number of reads per SAM file to buffer in memory" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--read_buffer_size"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Set the logging location" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--log_to_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "None\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-jar" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/usr/bin/gatk.jar"
]
[ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-T" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "FindCoveredIntervals"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-Xms$(Math.round(parseInt(runtime.ram)/1910))G"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-Xmx$(Math.floor(parseInt(runtime.ram)/1048) - 1)G"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-XX:-UseGCOverheadLimit"
]
[ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "-Djava.io.tmpdir=$(runtime.tmpdir)"
]
) ;
cwl:baseCommand ( "java" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,