@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 ExpressionTool: . rdfs:comment "\tReport depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bg" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" . rdfs:comment "Print the header from the A file prior to results.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-header" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom ".mapped_and_filtered.read_count.txt" . rdfs:comment "Query chromosome used to calculate percentage" ; sld:type xsd:string . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; cwl:default ".sorted.bam" ; sld:type xsd:string . rdfs:comment "Output file name. If not specified, the basename of the input file with the suffix specified in the suffix argument will be used." ; sld:type xsd:string , sld:null . rdfs:comment "If using BAM input, write output as BED.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bed" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_basename_file + '.masked.bam')" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tReport depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero\ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0\ncoverage by applying: \"grep -w 0$\" to the output.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-bga" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90 percent of A is covered OR 10 percent of B is covered.\nWithout -e, both fractions would have to be satisfied.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-e" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Write the original entry in B for each overlap.\n- Useful for knowing _what_ A overlaps. Restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wb" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" ] ; sld:type cwl:File . rdfs:comment "Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "only include reads with none of the bits set in INT set in FLAG [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . rdfs:comment "Preseq c_curve output files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")" ; sld:type xsd:string , sld:null . rdfs:comment "Sorted bed or BAM file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Bedfile containing ENCODE consensus blacklist regions to be excluded." ; sld:type cwl:File . rdfs:comment "Aligned BAM file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:comment "ChIP-seq - map - PCR Bottleneck Coefficients" ; 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:requirements [ a cwl:ScatterFeatureRequirement ] . rdfs:comment "Picard Java jar file" ; cwl:default "/usr/picard/picard.jar" ; sld:type xsd:string . rdfs:comment "Report end-to-end hits w/ <=v mismatches; ignore qualities" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . rdfs:comment "Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\nhttp://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\nuploaded to the Genome Browser as a custom track,\nBUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackline" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . rdfs:comment "File to be converted to BAM with samtools" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "Percentage of uniq reads from preseq c_curve output" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "MarkDuplicates" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('OUTPUT=' + inputs.output_filename + '.' + inputs.output_suffix)" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('METRICS_FILE='+inputs.output_filename + '.' + inputs.metrics_suffix)" ] [ CommandLineBinding:position 5 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('TMP_DIR='+runtime.tmpdir)" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/picard" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "idxstats" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.bam)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.bam.basename + \".idxstats\")" . rdfs:comment "-hist input is a text file containing the observed histogram \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-H" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Output filename used as basename" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . rdfs:comment "trim bases from 3' (right) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim3" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "Save the percentage in a file of the given name" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Provide a genome file to enforce consistent chromosome sort order\nacross input files. Only applies when used with -sorted option.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-g" ] ; sld:type xsd:boolean , sld:null . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:CommandLineTool ; rdfs:comment "Extract mapped reads from BAM file using Samtools flagstat command" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 10000 ; CommandLineBinding:shellQuote false ; cwl:valueFrom " | head -n1 | cut -f 1 -d ' '" ] ) ; cwl:baseCommand ( "samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Aligned file in BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" ] ; sld:type cwl:File . rdfs:comment "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" ] ; sld:type cwl:File . rdfs:comment "-verbose print more information \n" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean . rdfs:comment "When using multiple databases, provide an alias for each that\nwill appear instead of a fileId when also printing the DB record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-names" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "BAM files without duplicate reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-g" ] ; sld:type cwl:File . rdfs:comment "" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-b" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "read-count-from-bowtie-log.sh" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; 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:ShellCommandRequirement ] ; cwl:stdout "$(inputs.bowtie_log.path.replace(/^.*[\\\\\\/]/, '') + '.read_count.mapped')" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.' + inputs.metrics_suffix)" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.input_file.basename + '.bai')" ] ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:baseCommand ( "samtools" "index" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input_file)" ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations\nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-split" ] ; sld:type xsd:boolean , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Extracts the base name of a file" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "echo" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs . rdfs:comment "Require same strandedness. That is, only report hits in B\nthat overlap A on the _same_ strand.\n- By default, overlaps are reported without respect to strand.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Sort by read name" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:boolean . rdfs:comment "Idxstats output file. TAB-delimited with each line consisting of reference\nsequence name, sequence length, # mapped reads and # unmapped reads\n" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename + \".idxstats\")" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Bam file (it should be indexed)" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Usage: c_curve [OPTIONS] \n\nOptions:\n -o, -output yield output file (default: stdout) \n -s, -step step size in extrapolations (default: 1e+06) \n -v, -verbose print more information \n -P, -pe input is paired end read file \n -H, -hist input is a text file containing the observed histogram \n -V, -vals input is a text file containing only the observed counts \n -B, -bam input is in BAM format \n -l, -seg_len maximum segment length when merging paired end bam reads \n (default: 5000) \n\nHelp options:\n -?, -help print this help message \n -about print about message" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "preseq" "c_curve" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/preseq:2.0" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_file_basename + '.preseq_c_curve.txt')" . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Extracts the base name of a file" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "echo" ) ; cwl:baseCommand ( "echo" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [] ; sld:type cwl:File . rdfs:comment " number of alignment threads to launch (default: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--threads" ] ; sld:type xsd:int . sld:type xsd:string . rdfs:comment "Basename for the output file" ; sld:type xsd:string . rdfs:comment "JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:shellQuote false ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_basename + '.preseq_c_curve.txt')" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-b" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bam')" . rdfs:comment "trim bases from 5' (left) end of reads" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--trim5" ] ; sld:type xsd:int , sld:null . rdfs:comment "-seg_len maximum segment length when merging paired end bam reads \n(default: 5000)\nHelp options:\n-?, -help print this help message\n-about print about message\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:int , sld:null . rdfs:comment "First file (extension .1.ebwt) of the Bowtie index files generated for the reference genome (see http://bowtie-bio.sourceforge.net/tutorial.shtml#newi)" ; cwl:inputBinding [ CommandLineBinding:position 9 ; cwl:valueFrom "$(self.path.split('.').splice(0,self.path.split('.').length-2).join(\".\"))" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Write uncompressed BAM output. Default writes compressed BAM.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-ubam" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${return true}" . cwl:valueFrom "chrM" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Picard MarkDuplicates metrics files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sorted" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "-vals input is a text file containing only the observed counts \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-V" ] ; sld:type cwl:File , sld:null . rdfs:comment "Input format autodetected" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean . rdfs:comment "only include reads with mapping quality >= INT [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-q" ] ; sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "One or more input SAM or BAM files to analyze. Must be coordinate sorted." ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$('INPUT=' + self.path)" ] ; sld:type cwl:File . cwl:source . rdfs:comment "maximum insert size for paired-end alignment (default: 250)" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-X" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default false)." ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "BARCODE_TAG=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "Suffix used to identify the output file (Default: dedup.bam)" ; cwl:default "dedup.bam" ; sld:type xsd:string . rdfs:comment "Percentage of mitochondrial reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Require different strandedness. That is, only report hits in B\nthat overlap A on the _opposite_ strand.\n- By default, overlaps are reported without respect to strand.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "File to be converted to BAM with samtools" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.PBC.txt')" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Get number of processed reads from Bowtie log." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "percent-uniq-reads-from-preseq.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "reddylab/workflow-utils:ggr" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" . cwl:source . cwl:source . rdfs:comment "BAM files with marked duplicate reads." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "Write the original entry in A for each overlap.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wa" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files\nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nobuf" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Query input FASTQ file." ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . rdfs:comment "Write the original A entry _once_ if _any_ overlaps found in B.\n- In other words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-u" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Hits guaranteed best stratum; ties broken by quality" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--best" ] ; sld:type xsd:boolean . rdfs:comment "Read counts of the mapped and filtered BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:valueFrom "${return 2}" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.' + inputs.output_suffix)" ] ; sld:type cwl:File . cwl:source . rdfs:comment "-step step size in extrapolations (default: 1e+06) \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:float , sld:null . rdfs:comment "max mismatches in seed (between [0, 3], default: 2)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedmms" ] ; sld:type xsd:int , sld:null . rdfs:comment "\tReport the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-d" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "Writes additional track line definition parameters in the first line.\n- Example:\n-trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\nNote the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-trackopts" ] ; sld:type xsd:string , sld:null . rdfs:comment "When using multiple databases, sort the output DB hits\nfor each record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-sortout" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools genomecov (aka genomeCoverageBed)\nVersion: v2.25.0\nSummary: Compute the coverage of a feature file among a genome.\n\nUsage: bedtools genomecov [OPTIONS] -i -g \n\nOptions: \n\t-ibam\t\tThe input file is in BAM format.\n\t\t\tNote: BAM _must_ be sorted by position\n\n\t-d\t\tReport the depth at each genome position (with one-based coordinates).\n\t\t\tDefault behavior is to report a histogram.\n\n\t-dz\t\tReport the depth at each genome position (with zero-based coordinates).\n\t\t\tReports only non-zero positions.\n\t\t\tDefault behavior is to report a histogram.\n\n\t-bg\t\tReport depth in BedGraph format. For details, see:\n\t\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html\n\n\t-bga\t\tReport depth in BedGraph format, as above (-bg).\n\t\t\tHowever with this option, regions with zero \n\t\t\tcoverage are also reported. This allows one to\n\t\t\tquickly extract all regions of a genome with 0 \n\t\t\tcoverage by applying: \"grep -w 0$\" to the output.\n\n\t-split\t\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\n\t\t\twhen computing coverage.\n\t\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \n\t\t\tto infer the blocks for computing coverage.\n\t\t\tFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\n\t\t\tfields (i.e., columns 10,11,12).\n\n\t-strand\t\tCalculate coverage of intervals from a specific strand.\n\t\t\tWith BED files, requires at least 6 columns (strand is column 6). \n\t\t\t- (STRING): can be + or -\n\n\t-5\t\tCalculate coverage of 5\" positions (instead of entire interval).\n\n\t-3\t\tCalculate coverage of 3\" positions (instead of entire interval).\n\n\t-max\t\tCombine all positions with a depth >= max into\n\t\t\ta single bin in the histogram. Irrelevant\n\t\t\tfor -d and -bedGraph\n\t\t\t- (INTEGER)\n\n\t-scale\t\tScale the coverage by a constant factor.\n\t\t\tEach coverage value is multiplied by this factor before being reported.\n\t\t\tUseful for normalizing coverage by, e.g., reads per million (RPM).\n\t\t\t- Default is 1.0; i.e., unscaled.\n\t\t\t- (FLOAT)\n\n\t-trackline\tAdds a UCSC/Genome-Browser track line definition in the first line of the output.\n\t\t\t- See here for more details about track line definition:\n\t\t\t http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n\t\t\t- NOTE: When adding a trackline definition, the output BedGraph can be easily\n\t\t\t uploaded to the Genome Browser as a custom track,\n\t\t\t BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n\n\t-trackopts\tWrites additional track line definition parameters in the first line.\n\t\t\t- Example:\n\t\t\t -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\t\t\t Note the use of single-quotes if you have spaces in your parameters.\n\t\t\t- (TEXT)\n\nNotes: \n\t(1) The genome file should tab delimited and structured as follows:\n\t \n\n\tFor example, Human (hg19):\n\tchr1\t249250621\n\tchr2\t243199373\n\t...\n\tchr18_gl000207_random\t4262\n\n\t(2) The input BED (-i) file must be grouped by chromosome.\n\t A simple \"sort -k 1,1 > .sorted\" will suffice.\n\n\t(3) The input BAM (-ibam) file must be sorted by position.\n\t A \"samtools sort \" should suffice.\n\nTips: \n\tOne can use the UCSC Genome Browser's MySQL database to extract\n\tchromosome sizes. For example, H. sapiens:\n\n\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "genomecov" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.ibam.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + '.bdg')" . rdfs:comment "Filter unmapped reads in aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.accepted_hits.bam')" ] ; sld:type cwl:File . cwl:source . rdfs:comment "PCR Bottleneck Coeficient files." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Write the original A and B entries plus the number of base\npairs of overlap between the two features.\n- Overlapping features restricted by -f and -r.\nHowever, A features w/o overlap are also reported\nwith a NULL B feature and overlap = 0.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wao" ] ; sld:type xsd:boolean , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Number of threads used in sorting" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:valueFrom "${return true}" . sld:type xsd:string . rdfs:comment "output BAM" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-b" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Write hits in SAM format (default: BAM)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sam" ] ; sld:type xsd:boolean . cwl:source . cwl:default true . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.file_path.replace(/\\.[^/.]+$/, \"\"))" ] ; sld:type xsd:string . rdfs:comment "Indexed BAM file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "FILE only include reads overlapping this BED FILE [null]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:valueFrom "${return inputs.idxstats.basename.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '').replace(/\\.[^/.]+$/, '').replace(/\\.[^/.]+$/, '.mitochondrial_percentage.txt')}" . rdfs:comment "-bam input is in BAM format \n" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-B" ] ; sld:type xsd:boolean . rdfs:comment "\tCalculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6).\n- (STRING): can be + or -\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-strand" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:comment "Tool: bedtools intersect (aka intersectBed)\nVersion: v2.25.0\nSummary: Report overlaps between two feature files.\n\nUsage: bedtools intersect [OPTIONS] -a -b \n\n\tNote: -b may be followed with multiple databases and/or \n\twildcard (*) character(s). \nOptions: \n\t-wa\tWrite the original entry in A for each overlap.\n\n\t-wb\tWrite the original entry in B for each overlap.\n\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r.\n\n\t-loj\tPerform a \"left outer join\". That is, for each feature in A\n\t\treport each overlap with B. If no overlaps are found, \n\t\treport a NULL feature for B.\n\n\t-wo\tWrite the original A and B entries plus the number of base\n\t\tpairs of overlap between the two features.\n\t\t- Overlaps restricted by -f and -r.\n\t\t Only A features with overlap are reported.\n\n\t-wao\tWrite the original A and B entries plus the number of base\n\t\tpairs of overlap between the two features.\n\t\t- Overlapping features restricted by -f and -r.\n\t\t However, A features w/o overlap are also reported\n\t\t with a NULL B feature and overlap = 0.\n\n\t-u\tWrite the original A entry _once_ if _any_ overlaps found in B.\n\t\t- In other words, just report the fact >=1 hit was found.\n\t\t- Overlaps restricted by -f and -r.\n\n\t-c\tFor each entry in A, report the number of overlaps with B.\n\t\t- Reports 0 for A entries that have no overlap with B.\n\t\t- Overlaps restricted by -f and -r.\n\n\t-v\tOnly report those entries in A that have _no overlaps_ with B.\n\t\t- Similar to \"grep -v\" (an homage).\n\n\t-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\n\n\t-s\tRequire same strandedness. That is, only report hits in B\n\t\tthat overlap A on the _same_ strand.\n\t\t- By default, overlaps are reported without respect to strand.\n\n\t-S\tRequire different strandedness. That is, only report hits in B\n\t\tthat overlap A on the _opposite_ strand.\n\t\t- By default, overlaps are reported without respect to strand.\n\n\t-f\tMinimum overlap required as a fraction of A.\n\t\t- Default is 1E-9 (i.e., 1bp).\n\t\t- FLOAT (e.g. 0.50)\n\n\t-F\tMinimum overlap required as a fraction of B.\n\t\t- Default is 1E-9 (i.e., 1bp).\n\t\t- FLOAT (e.g. 0.50)\n\n\t-r\tRequire that the fraction overlap be reciprocal for A AND B.\n\t\t- In other words, if -f is 0.90 and -r is used, this requires\n\t\t that B overlap 90 percent of A and A _also_ overlaps 90 percent of B.\n\n\t-e\tRequire that the minimum fraction be satisfied for A OR B.\n\t\t- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\n\t\t that either 90 percent of A is covered OR 10 percent of B is covered.\n\t\t Without -e, both fractions would have to be satisfied.\n\n\t-split\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\n\n\t-g\tProvide a genome file to enforce consistent chromosome sort order\n\t\tacross input files. Only applies when used with -sorted option.\n\n\t-nonamecheck\tFor sorted data, don't throw an error if the file has different naming conventions\n\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\".\n\n\t-sorted\tUse the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n\n\t-names\tWhen using multiple databases, provide an alias for each that\n\t\twill appear instead of a fileId when also printing the DB record.\n\n\t-filenames\tWhen using multiple databases, show each complete filename\n\t\t\tinstead of a fileId when also printing the DB record.\n\n\t-sortout\tWhen using multiple databases, sort the output DB hits\n\t\t\tfor each record.\n\n\t-bed\tIf using BAM input, write output as BED.\n\n\t-header\tPrint the header from the A file prior to results.\n\n\t-nobuf\tDisable buffered output. Using this option will cause each line\n\t\tof output to be printed as it is generated, rather than saved\n\t\tin a buffer. This will make printing large output files \n\t\tnoticeably slower, but can be useful in conjunction with\n\t\tother software tools and scripts that need to process one\n\t\tline of bedtools output at a time.\n\n\t-iobuf\tSpecify amount of memory to use for input buffer.\n\t\tTakes an integer argument. Optional suffixes K/M/G supported.\n\t\tNote: currently has no effect with compressed files.\n\nNotes: \n\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,\n\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not\n\treported, as we are only testing for one or more overlaps." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bedtools" "intersect" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bedtools" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_basename_file + '.masked.bam')" . rdfs:comment "Perform a \"left outer join\". That is, for each feature in A\nreport each overlap with B. If no overlaps are found,\nreport a NULL feature for B.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-loj" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "\tCalculate coverage of 3\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-3" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Compute PCR Bottleneck Coeficient from BedGraph file." ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "awk" "$4==1 {N1 += $3 - $2}; $4>=1 {Nd += $3 - $2} END {print N1/Nd}" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:stdout "$(inputs.output_filename + '.PBC.txt')" . rdfs:comment "Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:float , sld:null . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . rdfs:comment "For sorted data, don't throw an error if the file has different naming conventions\nfor the same chromosome. ex. \"chr1\" vs \"chr01\".\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nonamecheck" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "\tScale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-scale" ] ; sld:type xsd:float , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" "-F" "4" "-b" "-h" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_filename + '.accepted_hits.bam')" . cwl:source . rdfs:comment "Sorted aligned file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + inputs.suffix)" ] ; sld:type cwl:File . rdfs:comment "Hits in sub-optimal strata aren't reported (requires --best)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--strata" ] ; sld:type xsd:boolean . rdfs:comment "Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder." ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "samtools" "view" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/samtools:1.3" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "${\n if (inputs.outfile_name) return inputs.outfile_name;\n var suffix = inputs.b ? '.bam' : '.sam';\n suffix = inputs.suffix || suffix;\n return inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + suffix\n}\n" . rdfs:comment "Input file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-a" ] ; sld:type cwl:File . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90 percent of A and A _also_ overlaps 90 percent of B.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-r" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 11 ; cwl:valueFrom "$(inputs.output_filename + '.sam')" ] ) ; cwl:baseCommand ( "bowtie" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/bowtie" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.output_filename + '.bowtie.log')" . rdfs:comment "\tThe input file is in BAM format.\nNote: BAM _must_ be sorted by position\n" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-ibam" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "\tReport the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-dz" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Write the original A and B entries plus the number of base\npairs of overlap between the two features.\n- Overlaps restricted by -f and -r.\nOnly A features with overlap are reported.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-wo" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Samtools idxstats file" ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . rdfs:comment "Input format autodetected" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-S" ] ; sld:type xsd:boolean . rdfs:comment "Read counts of the mapped BAM files" ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:valueFrom ".dedup.bam" . rdfs:comment "\tCombine all positions with a depth >= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-max" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "suffix of the transformed SAM/BAM file (including extension, e.g. .filtered.sam)" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Suffix used to create the metrics output file (Default: dedup_metrics.txt)" ; cwl:default "dedup_metrics.txt" ; sld:type xsd:string . rdfs:comment "uncompressed BAM output (implies -b)" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-u" ] ; sld:type xsd:boolean . rdfs:comment "Path to the picard.jar file" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-jar" ] ; sld:type xsd:string . cwl:valueFrom "bam" . rdfs:comment "Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ] ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "Suppress all alignments if > exist (def: 1)" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-m" ] ; sld:type xsd:int . cwl:valueFrom "${return 2000}" . rdfs:comment "\tCalculate coverage of 5\" positions (instead of entire interval).\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-5" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . rdfs:comment "When using multiple databases, show each complete filename\ninstead of a fileId when also printing the DB record.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-filenames" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Aligned file to be sorted with samtools" ; cwl:inputBinding [ CommandLineBinding:position 1000 ] ; sld:type cwl:File . rdfs:comment "The number of megabytes of memory a given thread is given to store path descriptors in --best mode. (Default: 256)" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--chunkmbs" ] ; sld:type xsd:int , sld:null . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var regExp = new RegExp(inputs.chrom + \"\\\\s\\\\d+\\\\s(\\\\d+)\\\\s(\\\\d+)\");\n var match = inputs.idxstats.contents.match(regExp);\n if (match){\n var chrom_mapped_reads = match[1];\n var total_reads = inputs.idxstats.contents.split(\"\\n\")\n .map(function(x){\n var rr = x.match(/.*\\s\\d+\\s(\\d+)\\s\\d+/);\n return (rr ? rr[1] : 0);\n })\n .reduce(function(a, b) { return Number(a) + Number(b); });\n\n var output = (100*chrom_mapped_reads/total_reads).toFixed(4) + \"%\" + \"\\n\";\n\n if (inputs.output_filename){\n return {\n percent_map : {\n \"class\": \"File\",\n \"basename\" : inputs.output_filename,\n \"contents\" : output,\n }\n }\n }\n return output;\n }\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:valueFrom "${return inputs.input_file.basename.replace('dups_marked', 'dedup')}" . cwl:inputBinding [] ; sld:type cwl:File . rdfs:comment "Include header in output" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-h" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "If true do not write duplicates to the output file instead of writing them with appropriate flags set. (Default false)." ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$('REMOVE_DUPLICATES=' + self)" ] ; sld:type xsd:boolean . rdfs:comment "For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Genome sizes tab-delimited file (used in samtools)" ; sld:type cwl:File . cwl:valueFrom ".dups_marked.bam" . cwl:source . sld:type xsd:string . cwl:source . sld:type cwl:File , xsd:string . rdfs:comment "Samtools Flagstat report file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_bam_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + inputs.output_suffix)" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:valueFrom "${return 1024}" . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:source . rdfs:comment "Aligned file in SAM or BAM format" ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.outfile_name) return inputs.outfile_name;\n var suffix = inputs.b ? '.bam' : '.sam';\n suffix = inputs.suffix || suffix;\n return inputs.input_file.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, '') + suffix\n}\n" ] ; sld:type cwl:File . rdfs:comment "-pe input is paired end read file \n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-P" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Input fastq files" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Bowtie log file." ; cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Number of threads used" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-@" ] ; sld:type xsd:int . cwl:source . rdfs:comment "Print wall-clock time taken by search phases" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:boolean . rdfs:comment "only include reads with all bits set in INT set in FLAG [0]" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:comment "ATAC-seq 03 mapping - reads: SE - blacklist removal" ; 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:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . rdfs:comment "seed length for -n (default: 28)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--seedlen" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.bowtie.log')" ] ; sld:type cwl:File . rdfs:comment "Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-iobuf" ] ; sld:type xsd:int , sld:null . cwl:default 1 ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preseq_c_curve_outfile.path.replace(/^.*[\\\\\\/]/, '').replace(/\\.[^/.]+$/, \"\") + '.percentage_unique_reads.txt')" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . rdfs:comment "Aligned bowtie file in [SAM|BAM] format." ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename + '.sam')" ] ; sld:type cwl:File .