Common Workflow Language Viewer

https://view.commonwl.org

Mark Robinson

Stian Soiland-Reyes 

Michael Crusoe

Carole Goble

http://slides.com/markrobinson/cwlviewer

 http://orcid.org/0000-0002-8184-7507
http://orcid.org/0000-0001-9842-9718
http://orcid.org/0000-0002-2961-9670
http://orcid.org/0000-0003-1219-2137

@soilandreyes

These slides are licensed under a
Creative Commons Attribution 4.0 International License

2017-07-22 BOSC 2017
ISMB/ECCB 2017, Prague

Difficulties in sharing CWL

Workflow spread over multiple text files

https://github.com/common-workflow-language/

workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl

Difficulties in sharing CWL

Often missing:

 

Detailed description (what, how)

Provenance (who, where, when)

Versioning (which)

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow

inputs:
  #SCWRL
  scw_script: File
  scw_input_pdb_path: File
  scw_output_pdb_path: string
  scw_mutation: string
  scw_scwrl_path: string
  scw_log_path: string
  scw_error_path: string
  #PDB2GMX
  p2g_script: File
  p2g_output_gro_path: string
  p2g_output_top_path: string
  p2g_output_itp_path: string
  p2g_output_top_tar_path: string
  p2g_water_type: string
  p2g_force_field: string
  p2g_ignh: string
  p2g_gmx_path: string
  p2g_log_path: string
  p2g_error_path: string
  # ...

We need better incentives!

#!/usr/bin/env cwl-runner
cwlVersion: "cwl:draft-3"

class: Workflow

inputs:
  - id: p1
    type:
      - "null"
      - type: array
        items: File
    description: list of files containing the first end of paired end reads in fasta or fastq format

  - id: p2
    type:
      - "null"
      - type: array
        items: File
    description: list of files containing the second end of paired end reads in fasta or fastq format

  - id: output_prefix
    type: string
    description: prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats

  - id: reference
    type: File
    description: "lobSTR's bwa reference files"

  - id: rg-sample
    type: string
    description: Use this in the read group SM tag

  - id: rg-lib
    type: string
    description: Use this in the read group LB tag

  - id: strinfo
    type: File
    description: File containing statistics for each STR.

  - id: noise_model
    type: File
    description: File to read noise model parameters from (.stepmodel)
    secondaryFiles:
      - "^.stuttermodel"

outputs:
  - id: bam
    type: File
    source: "#samindex/bam_with_bai"

  - id: bam_stats
    type: File
    source: "#lobSTR/bam_stats"

  - id: vcf
    type: File
    source: "#allelotype/vcf"

  - id: vcf_stats
    type: File
    source: "#allelotype/vcf_stats"

hints:
  - class: DockerRequirement
    dockerLoad: https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-x2ae13tsx5jqg8d/1nduktd8dpvhdpgsva82lje0i710kgzb6rttks5jldx7s2y7k9/7e0c0ae3bf4e70442f9b8eee816ec23426d9e1169a2925316e5c932745e21613.tar
    dockerImageId: 7e0c0ae3bf4e70442f9b8eee816ec23426d9e1169a2925316e5c932745e21613

steps:
  - id: lobSTR
    run: lobSTR-tool.cwl
    inputs:
      - { id: p1, source: "#p1" }
      - { id: p2, source: "#p2" }
      - { id: output_prefix, source: "#output_prefix" }
      - { id: reference, source: "#reference" }
      - { id: rg-sample, source: "#rg-sample" }
      - { id: rg-lib, source: "#rg-lib" }
    outputs:
      - { id: bam }
      - { id: bam_stats }

  - id: samsort
    run: samtools-sort.cwl
    inputs:
      - { id: input, source: "#lobSTR/bam" }
      - { id: output_name, default: "aligned.sorted.bam" }
    outputs:
      - { id: output_file }

  - id: samindex
    run: samtools-index.cwl
    inputs:
      - { id: input, source: "#samsort/output_file" }
    outputs:
      - { id: bam_with_bai }

  - id: allelotype
    run: allelotype.cwl
    inputs:
      - { id: bam, source: "#samindex/bam_with_bai" }
      - { id: reference, source: "#reference" }
      - { id: output_prefix, source: "#output_prefix" }
      - { id: noise_model, source: "#noise_model" }
      - { id: strinfo, source: "#strinfo" }
    outputs:
      - { id: vcf }
      - { id: vcf_stats }

Visualisation = quick and easy understanding

CWL Viewer

https://view.commonwl.org

View a Workflow

https://view.commonwl.org/workflows/github.com/common-workflow-language/workflows/blob/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl

Interactivity

https://view.commonwl.org/workflows/github.com/ProteinsWebTeam/ebi-metagenomics-cwl/tree/master/tools/rRNA_selection.cwl

Download and Share

Visualisation Images

(various formats)

GraphViz DOT source

Research Object Bundle/

Origin Information

A Research Object bundles and relates digital resources of a scientific experiment or investigation:​

 

Data used and results produced in experimental study​

Methods employed to produce and analyse that data​

Provenance and settings for the experiments​

People involved in the investigation​

Annotations about these resources, to improve understanding and interpretation

bundle.zip
├── mimetype
├── .ro
│   └── manifest.json
└── workflow
    ├── completeWorkflow.cwl
    ├── concatFasta.cwl
    ├── fastqc.cwl
    ├── generateRReports.cwl
    ├── qiimeAddMetadata.cwl
    ├── readPair.yml
    ├── uparseChimeraCheck.cwl
    ├── uparseDerepWorkAround.cwl
    ├── uparseFastqMerge.cwl
    ├── uparseFilter.cwl
    └── uparseTruncateLength.cwl
{
  "@context" : [ "https://w3id.org/bundle/context" ],
  "id" : "/",
  "manifest" : [ "manifest.json" ],
  "createdOn" : "2017-02-27T11:48:54.986Z",
  "createdBy" : {
    "uri" : "http://view.commonwl.org",
    "name" : "Common Workflow Language Viewer"
  },
  "authoredBy" : [ {
    "uri" : "https://github.com/grbot",
    "name" : "Gerrit Botha"
  }, {
    "uri" : "https://github.com/mr-c",
    "name" : "Michael R. Crusoe"
  }, {
    "name" : "Ubuntu"
  }, {
    "uri" : "https://github.com/mepstein-gh",
    "name" : "Milt Epstein"
  }, {
    "uri" : "https://github.com/ShakunBaichoo",
    "name" : "ShakunBaichoo"
  } ],
  "importedFrom" : "https://github.com/h3abionet/h3abionet16S/tree/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows",
  "importedOn" : "2017-02-27T11:48:54.986Z",
  "importedBy" : {
    "uri" : "http://view.commonwl.org",
    "name" : "Common Workflow Language Viewer"
  },
  "aggregates" : [ {
    "uri" : "/workflow/completeWorkflow.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:55.21Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mr-c",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/completeWorkflow.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:fbc4f48a-b111-4e1b-b6b9-d6a97c7c7f90",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/concatFasta.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:55.406Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/concatFasta.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:a9576413-03e7-42c1-8a78-0bcc888fbe2b",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/fastqc.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:55.545Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/fastqc.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:6a1a449c-d577-4d8c-9810-e919a7df79ab",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/generateRReports.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:55.701Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/generateRReports.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:e44f044a-b30a-4669-b1db-f06504db5752",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeAddMetadata.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:55.85Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeAddMetadata.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:bd30d107-7e4f-4f1d-b54d-6537b6756482",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeAlignSeqs.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.007Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeAlignSeqs.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:3630c7e2-0f81-4ca1-8992-78fa7206dab2",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeAssignTaxonomy.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.198Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeAssignTaxonomy.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:78d24ee4-a936-4b53-87e1-a0663f2540f4",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeFilterAlign.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.34Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeFilterAlign.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:06239baa-761c-40e9-bc31-c6646f6ccfe7",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeMakePhylogeny.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.544Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeMakePhylogeny.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:ac75b37c-322f-4277-adf0-755fe4d30334",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeOtusTxt2Biom.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.746Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeOtusTxt2Biom.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:ed3b2548-6749-420b-8f01-8b2084c90e9a",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeSummaryObservations.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:56.895Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeSummaryObservations.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:a8875d98-d43e-44b2-a290-fdb2f2e7b01e",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/qiimeSummaryQualitative.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:57.033Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/qiimeSummaryQualitative.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:412306bb-419f-46f2-a279-85ec98526ab2",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/readPair.yml",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-02-27T11:48:57.835Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mr-c",
      "name" : "Michael R. Crusoe"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/readPair.yml",
    "bundledAs" : {
      "uri" : "urn:uuid:3f3681b9-03a8-45ea-b278-ee59223813bc",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/uparseChimeraCheck.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:57.98Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/uparseChimeraCheck.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:1a848cc0-f942-407f-a23f-5654c4f9fa43",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/uparseDerepWorkAround.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:58.113Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/uparseDerepWorkAround.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:2b551c93-b5e2-498c-9aba-a4fce586ffdd",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/uparseFastqMerge.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:58.243Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/uparseFastqMerge.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:282307ca-cc45-4dcb-afdd-9b94183ccc25",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/uparseFilter.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:58.432Z",
    "authoredBy" : [ {
      "uri" : "https://github.com/grbot",
      "name" : "Gerrit Botha"
    }, {
      "uri" : "https://github.com/mepstein-gh",
      "name" : "Milt Epstein"
    }, {
      "uri" : "https://github.com/ShakunBaichoo",
      "name" : "ShakunBaichoo"
    } ],
    "retrievedFrom" : "https://github.com/h3abionet/h3abionet16S/blob/70498847fd6bfc63f44c59c748233cac7f8dd85d/workflows/uparseFilter.cwl",
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:dcdbf23f-7cb4-4214-9162-29ddcaf13d37",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/uparseGlobalSearchWorkAround.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-02-27T11:48:58.573Z",
    "authoredBy" : [ {
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    }, {
      "name" : "Ubuntu"
    } ],
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}

Provenance, attribution

 

Who made which part of the workflow when

CWL Viewer Research Objects

BOSC 2017
Birds of a Feather

 

Today 12:20-13:40
BoF #2: Common Workflow Language community meetup

 

Farah Zaib Khan & Stian Soiland-Reyes:

ResearchObject.org & CWL integration

Discovery of Workflows

https://view.commonwl.org/workflows

In the Works!

JSON API

Use of the cwltool reference implementation for parsing

Input labelling

More import options

And More!

cwl-svg

https://view.commonwl.org/

Join us!

Poster (A-124):
https://doi.org/10.7490/f1000research.1114375.1

https://github.com/
common-workflow-language/cwlviewer

Common Workflow Language Viewer

By Mark Robinson

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Common Workflow Language Viewer

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