Skip to content

Not producing cwl:source links for valid workflow in --print-rdf #431

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
MarkRobbo opened this issue Jun 16, 2017 · 4 comments
Closed

Not producing cwl:source links for valid workflow in --print-rdf #431

MarkRobbo opened this issue Jun 16, 2017 · 4 comments

Comments

@MarkRobbo
Copy link
Member

MarkRobbo commented Jun 16, 2017 •
edited
Loading

Expected Behavior

cwl:source predicates exist to define the links between steps

Actual Behavior

No such links are present so steps are disconnected:

cwlviewer graph

Workflow Code

https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl

cwltool --print-rdf https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl

Produces:

@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix CommandLineTool: <https://w3id.org/cwl/cwl#CommandLineTool/> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix CreateFileRequirement: <https://w3id.org/cwl/cwl#CreateFileRequirement/> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix EnvVarRequirement: <https://w3id.org/cwl/cwl#EnvVarRequirement/> .
@prefix EnvironmentDef: <https://w3id.org/cwl/cwl#EnvironmentDef/> .
@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .
@prefix File: <https://w3id.org/cwl/cwl#File/> .
@prefix FileDef: <https://w3id.org/cwl/cwl#FileDef/> .
@prefix InlineJavascriptRequirement: <https://w3id.org/cwl/cwl#InlineJavascriptRequirement/> .
@prefix JsonldPredicate: <https://w3id.org/cwl/salad#JsonldPredicate/> .
@prefix LinkMergeMethod: <https://w3id.org/cwl/cwl#LinkMergeMethod/> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@prefix SaladRecordSchema: <https://w3id.org/cwl/salad#SaladRecordSchema/> .
@prefix ScatterMethod: <https://w3id.org/cwl/cwl#ScatterMethod/> .
@prefix SchemaBase: <https://w3id.org/cwl/cwl#SchemaBase/> .
@prefix SchemaDefRequirement: <https://w3id.org/cwl/cwl#SchemaDefRequirement/> .
@prefix SchemaDefinedType: <https://w3id.org/cwl/salad#SchemaDefinedType/> .
@prefix Sink: <https://w3id.org/cwl/cwl#Sink/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix cwl: <https://w3id.org/cwl/cwl#> .
@prefix ns1: <rdfs:> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sld: <https://w3id.org/cwl/salad#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl> a cwl:Workflow ;
    Workflow:steps <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#allelotype>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#samindex>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#samsort> ;
    cwl:cwlVersion <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/v1.1.0-dev1> ;
    cwl:hints [ a cwl:DockerRequirement ;
            DockerRequirement:dockerImageId "7e0c0ae3bf4e70442f9b8eee816ec23426d9e1169a2925316e5c932745e21613" ;
            DockerRequirement:dockerLoad "https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-x2ae13tsx5jqg8d/1nduktd8dpvhdpgsva82lje0i710kgzb6rttks5jldx7s2y7k9/7e0c0ae3bf4e70442f9b8eee816ec23426d9e1169a2925316e5c932745e21613.tar" ] ;
    cwl:inputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#noise_model>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#output_prefix>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#p1>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#p2>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#reference>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#rg-lib>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#rg-sample>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#strinfo> ;
    cwl:outputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#bam>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#bam_stats>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#vcf>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#vcf_stats> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl> a cwl:CommandLineTool ;
    cwl:arguments ( "--noweb" ) ;
    cwl:baseCommand ( "allelotype" "--command" "classify" ) ;
    cwl:cwlVersion <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/v1.1.0-dev1> ;
    cwl:inputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#bam>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#noise_model>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#output_prefix>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#reference>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#strinfo> ;
    cwl:outputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#vcf>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#vcf_stats> ;
    cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
    sld:doc "Run lobSTR allelotype classifier." .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#bam> cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ;
    cwl:secondaryFiles ".bai" ;
    sld:doc """BAM file to analyze. Should have a unique read group and be sorted and indexed.
""" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#noise_model> cwl:inputBinding [ CommandLineBinding:prefix "--noise_model" ;
            cwl:valueFrom """${ return {"path": self.path.match(/(.*)\\.stepmodel/)[1], "class": "File"}; }
""" ] ;
    cwl:secondaryFiles "^.stuttermodel" ;
    sld:doc """File to read noise model parameters from (.stepmodel)
""" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#output_prefix> cwl:inputBinding [ CommandLineBinding:prefix "--out" ] ;
    sld:doc "Prefix for output files. will output prefix.vcf and prefix.genotypes.tab" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#reference> cwl:inputBinding [ CommandLineBinding:prefix "--index-prefix" ;
            cwl:valueFrom """${ return {"path": self.path.match(/(.*)ref\\.fasta/)[1], "class": "File"}; }
""" ] ;
    cwl:secondaryFiles "${return self.location.replace(/(.*)ref\\.fasta/, \"$1chromsizes.tab\")}",
        "${return self.location.replace(/(.*)ref\\.fasta/, \"$1mergedref.bed\")}",
        "${return self.location.replace(/(.*)ref\\.fasta/, \"$1ref_map.tab\")}",
        ".amb",
        ".ann",
        ".bwt",
        ".pac",
        ".rbwt",
        ".rpac",
        ".rsa" ;
    sld:doc "lobSTR's bwa reference files" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#strinfo> cwl:inputBinding [ CommandLineBinding:prefix "--strinfo" ] ;
    sld:doc """File containing statistics for each STR.
""" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#vcf> cwl:outputBinding [ CommandOutputBinding:glob "$(inputs['output_prefix'] + '.vcf')" ] ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl#vcf_stats> cwl:outputBinding [ CommandOutputBinding:glob "$(inputs['output_prefix'] + '.allelotype.stats')" ] ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl> a cwl:CommandLineTool ;
    cwl:arguments ( "--verbose" "--noweb" [ cwl:valueFrom """${
  var r = /.*(\\.fastq|\\.fq)(\\.gz)?$/i;
  var m;
  if (inputs['files']) {
    m = r.exec(inputs.files[0].path);
  } else {
    m = r.exec(inputs.p1[0].path);
  }
  if (m) {
    if (m[2]) {
      return ["--fastq", "--gzip"];
    } else {
      return "--fastq";
    }
  } else {
    return null;
  }
}
""" ] [ cwl:valueFrom """${
  if (inputs['files'] && (/.*\\.bam$/i).test(inputs['files'][0].path) && !inputs.bampair) {
    return "--bam";
  } else {
    return null;
  }
}
""" ] ) ;
    cwl:baseCommand ( "lobSTR" ) ;
    cwl:cwlVersion <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/v1.1.0-dev1> ;
    cwl:inputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bampair>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bwaq>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#e>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#entropy-threshold>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#extend>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#fft-window-size>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#fft-window-step>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#files>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#g>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#maq>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-diff-ref>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-hits-quit-aln>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-read-length>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#maxflank>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#min-flank-allow-mismatch>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#min-read-length>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#minflank>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#mismatch>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#multi>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#oldillumina>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#output_prefix>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#p1>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#p2>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#r>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#reference>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#rg-lib>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#rg-sample>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#u> ;
    cwl:outputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bam>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bam_stats> ;
    cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
    sld:doc "lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data." ;
    ns1:
 "lobSTR" .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bam> cwl:outputBinding [ CommandOutputBinding:glob "$(inputs['output_prefix'] + '.aligned.bam')" ] ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bam_stats> cwl:outputBinding [ CommandOutputBinding:glob "$(inputs['output_prefix'] + '.aligned.stats')" ] ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bampair> cwl:inputBinding [ CommandLineBinding:prefix "--bampair" ] ;
    sld:doc """Reads are in BAM format and are paired-end. NOTE: BAM file MUST be sorted or collated by read name.
""" ;
    sld:type xsd:boolean,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#bwaq> cwl:inputBinding [ CommandLineBinding:prefix "--bwaq" ] ;
    sld:doc "trim reads based on quality score. Same as the -q parameter in BWA" ;
    sld:type xsd:int,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#e> cwl:default 1 ;
    cwl:inputBinding [ CommandLineBinding:prefix "-e" ] ;
    sld:doc "Maximum number of gap extends allowed in each flanking region" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#entropy-threshold> cwl:default 4.5e-01 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--entropy-threshold" ] ;
    sld:doc "Threshold score to call a window periodic" ;
    sld:type xsd:float .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#extend> cwl:default 1000 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--extend" ] ;
    sld:doc "Number of bp the reference was extended when building the index. Must be same as --extend parameter used to run lobstr_index.py" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#fft-window-size> cwl:default 16 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--fft-window-size" ] ;
    sld:doc "Size of sliding entropy window" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#fft-window-step> cwl:default 4 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--fft-window-step" ] ;
    sld:doc "Step size of the sliding window" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#files> cwl:inputBinding [ CommandLineBinding:itemSeparator "," ;
            CommandLineBinding:position 2 ;
            CommandLineBinding:prefix "--files" ] ;
    sld:doc "List of files of single ends in fasta, fastq, or BAM files to align. Also use this parameter to specify paired-end BAM files to align." ;
    sld:type [ sld:items cwl:File ;
            sld:type sld:array ],
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#g> cwl:default 1 ;
    cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ;
    sld:doc "Maximum number of gap opens allowed in each flanking region" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#maq> cwl:default 100 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--mapq" ] ;
    sld:doc "maximum allowed mapq score calculated as the sum of qualities at base mismatches" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-diff-ref> cwl:default 50 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--max-diff-ref" ] ;
    sld:doc "Only report reads differing by at most this number of bp from the reference allele" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-hits-quit-aln> cwl:default 1000 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--max-hits-quit-aln" ] ;
    sld:doc "Stop alignment search after this many hits found. Use -1 for no limit." ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#max-read-length> cwl:default 1024 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--min-read-length" ] ;
    sld:doc "Don't process reads longer than this" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#maxflank> cwl:default 100 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--maxflank" ] ;
    sld:doc "Length to trim flanking regions to before aligning" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#min-flank-allow-mismatch> cwl:default 30 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--min-flank-allow-mismatch" ] ;
    sld:doc "Don't allow mismatches if aligning flanking regions shorter than this" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#min-read-length> cwl:default 45 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--min-read-length" ] ;
    sld:doc "Don't process reads shorter than this" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#minflank> cwl:default 8 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--minflank" ] ;
    sld:doc "Minimum length of flanking region to try to align" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#mismatch> cwl:default 1 ;
    cwl:inputBinding [ CommandLineBinding:prefix "--mismatch" ] ;
    sld:doc "allowed edit distance in either flanking region" ;
    sld:type xsd:int .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#multi> cwl:inputBinding [ CommandLineBinding:prefix "--multi" ] ;
    sld:doc "Report reads mapping to multiple genomic locations" ;
    sld:type xsd:boolean,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#oldillumina> cwl:inputBinding [ CommandLineBinding:prefix "--oldillumina" ] ;
    sld:doc """specifies that base pair quality scores are reported in the old Phred
format (Illumina 1.3+, Illumina 1.5+) where quality scores are given as
Phred + 64 rather than Phred + 33
""" ;
    sld:type xsd:boolean,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#output_prefix> cwl:inputBinding [ CommandLineBinding:prefix "--out" ] ;
    sld:doc "prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#p1> cwl:inputBinding [ CommandLineBinding:itemSeparator "," ;
            CommandLineBinding:position 2 ;
            CommandLineBinding:prefix "--p1" ] ;
    sld:doc "list of files containing the first end of paired end reads in fasta or fastq format" ;
    sld:type [ sld:items cwl:File ;
            sld:type sld:array ],
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#p2> cwl:inputBinding [ CommandLineBinding:itemSeparator "," ;
            CommandLineBinding:position 3 ;
            CommandLineBinding:prefix "--p2" ] ;
    sld:doc "list of files containing the second end of paired end reads in fasta or fastq format" ;
    sld:type [ sld:items cwl:File ;
            sld:type sld:array ],
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#r> cwl:default -1 ;
    cwl:inputBinding [ CommandLineBinding:prefix "-e" ] ;
    sld:doc "fraction of missing alignments given 2% uniform base error rate. Ignored if --mismatch is set" ;
    sld:type xsd:float .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#reference> cwl:inputBinding [ CommandLineBinding:prefix "--index-prefix" ;
            cwl:valueFrom """${ return {"path": self.path.match(/(.*)ref\\.fasta/)[1], "class": "File"}; }
""" ] ;
    cwl:secondaryFiles "${return self.location.replace(/(.*)ref\\.fasta/, \"$1chromsizes.tab\");}",
        "${return self.location.replace(/(.*)ref\\.fasta/, \"$1mergedref.bed\");}",
        "${return self.location.replace(/(.*)ref\\.fasta/, \"$1ref_map.tab\");}",
        ".amb",
        ".ann",
        ".bwt",
        ".pac",
        ".rbwt",
        ".rpac",
        ".rsa",
        ".sa" ;
    sld:doc "lobSTR's bwa reference files" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#rg-lib> cwl:inputBinding [ CommandLineBinding:prefix "--rg-lib" ] ;
    sld:doc "Use this in the read group LB tag" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#rg-sample> cwl:inputBinding [ CommandLineBinding:prefix "--rg-sample" ] ;
    sld:doc "Use this in the read group SM tag" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl#u> cwl:inputBinding [ CommandLineBinding:prefix "-u" ] ;
    sld:doc "only report reads different by an integer number of copy numbers from the reference allele" ;
    sld:type xsd:boolean,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#allelotype> cwl:run <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/allelotype.cwl> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#bam> sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#bam_stats> sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR> cwl:run <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-tool.cwl> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#noise_model> cwl:secondaryFiles "^.stuttermodel" ;
    sld:doc "File to read noise model parameters from (.stepmodel)" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#> sld:doc "prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#p1> sld:doc "list of files containing the first end of paired end reads in fasta or fastq format" ;
    sld:type [ sld:items cwl:File ;
            sld:type sld:array ],
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#p2> sld:doc "list of files containing the second end of paired end reads in fasta or fastq format" ;
    sld:type [ sld:items cwl:File ;
            sld:type sld:array ],
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#reference> sld:doc "lobSTR's bwa reference files" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#rg-lib> sld:doc "Use this in the read group LB tag" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#rg-sample> sld:doc "Use this in the read group SM tag" ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#samindex> cwl:run <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#samsort> cwl:run <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl> .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#strinfo> sld:doc "File containing statistics for each STR." ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#vcf> sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl#vcf_stats> sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl> a cwl:CommandLineTool ;
    cwl:arguments ( "indexed.bam" ) ;
    cwl:baseCommand ( "samtools" "index" ) ;
    cwl:cwlVersion <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/v1.1.0-dev1> ;
    cwl:inputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl#input> ;
    cwl:outputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl#bam_with_bai> ;
    cwl:requirements [ a <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/InitialWorkDirRequirement> ] ;
    sld:doc "Invoke 'samtools index' to create a 'BAI' index (samtools 1.19)" .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl#bam_with_bai> cwl:outputBinding [ CommandOutputBinding:glob "indexed.bam" ] ;
    cwl:secondaryFiles ".bai" ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-index.cwl#input> sld:doc "Input bam file." ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl> a cwl:CommandLineTool ;
    cwl:arguments ( "-f" ) ;
    cwl:baseCommand ( "samtools" "sort" ) ;
    cwl:cwlVersion <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/v1.1.0-dev1> ;
    cwl:inputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#compression_level>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#input>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#memory>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#output_name>,
        <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#sort_by_name> ;
    cwl:outputs <https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#output_file> ;
    sld:doc "Invoke 'samtools sort' (samtools 1.19)" .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#compression_level> cwl:inputBinding [ CommandLineBinding:prefix "-l" ] ;
    sld:doc """Set the desired compression level for the final output file, ranging from
0 (uncompressed) or 1 (fastest but minimal compression) to 9 (best
compression but slowest to write), similarly to gzip(1)'s compression
level setting.

If -l is not used, the default compression level will apply.
""" ;
    sld:type xsd:int,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#input> cwl:inputBinding [ CommandLineBinding:position 1 ] ;
    sld:doc "Input bam file." ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#memory> cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ;
    sld:doc """Approximately the maximum required memory per thread, specified  in
bytes.
""" ;
    sld:type xsd:int,
        sld:null .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#output_file> cwl:outputBinding [ CommandOutputBinding:glob "$(inputs['output_name'])" ] ;
    sld:type cwl:File .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#output_name> cwl:inputBinding [ CommandLineBinding:position 2 ] ;
    sld:doc "Desired output filename." ;
    sld:type xsd:string .

<https://github.com/raw/common-workflow-language/workflows/master/workflows/lobSTR/samtools-sort.cwl#sort_by_name> cwl:inputBinding [ CommandLineBinding:prefix "-n" ] ;
    sld:doc "Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates." ;
    sld:type xsd:boolean,
        sld:null .

cwltool version

  • 1.0.20170525215327
@MarkRobbo
Copy link
Member Author

Found another example of this:

https://github.com/Duke-GCB/GGR-cwl/blob/master/ChIP-seq_pipeline/03-map-pe.cwl

http://i.imgur.com/9Aq33qW.png

@MarkRobbo
Copy link
Member Author

https://github.com/bmeg/funnel-client/blob/master/test/hashsplitter-workflow.cwl

Seems like a draft-3 exclusive bug

@mr-c
Copy link
Member

mr-c commented Aug 10, 2017

@MarkRobbo That'd be welcome news, we're deprecating draft-3 and draft-2 from the ref runner

@manu-chroma manu-chroma mentioned this issue Aug 14, 2017
Merged
@anton-khodak
Copy link
Member

Closed in #520

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@mr-c @MarkRobbo @anton-khodak