Stian Soiland-Reyes

(channelling Carole Goble, Michael Crusoe, Adam Hospital)

eScience lab, The University of Manchester

@soilandreyes

https://orcid.org/0000-0001-9842-9718

https://slides.com/soilandreyes/

Pistoia Symposium:
Application of Bioinformatics
in support of Precision Medicine
2019-03-11, London

This work has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728

Sharing reproducible computational analyses

Workflows

Containers

Repositories

 

Workflows

Findable

Accessible

Interoperable

Reusable

Inner FAIR

cwlVersion: v1.0
class: Workflow
inputs:
  inp: File
  ex: string

outputs:
  classout:
    type: File
    outputSource: compile/classfile

steps:
  untar:
    run: tar-param.cwl
    in:
      tarfile: inp
      extractfile: ex
    out: [example_out]

  compile:
    run: arguments.cwl
    in:
      src: untar/example_out
    out: [classfile]
cwlVersion: v1.0
class: Workflow
label: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

requirements:
 - class: SubworkflowFeatureRequirement
 - class: SchemaDefRequirement
   types: 
    - $import: ../tools/FragGeneScan-model.yaml
    - $import: ../tools/trimmomatic-sliding_window.yaml
    - $import: ../tools/trimmomatic-end_mode.yaml
    - $import: ../tools/trimmomatic-phred.yaml

inputs:
  reads:
    type: File
    format: edam:format_1930  # FASTQ

outputs:
  processed_sequences:
    type: File
    outputSource: clean_fasta_headers/sequences_with_cleaned_headers

steps:
  trim_quality_control:
    doc: |
      Low quality trimming (low quality ends and sequences with < quality scores
      less than 15 over a 4 nucleotide wide window are removed)
    run: ../tools/trimmomatic.cwl
    in:
      reads1: reads
      phred: { default: '33' }
      leading: { default: 3 }
      trailing: { default: 3 }
      end_mode: { default: SE }
      minlen: { default: 100 }
      slidingwindow:
        default:
          windowSize: 4
          requiredQuality: 15
    out: [reads1_trimmed]

  convert_trimmed-reads_to_fasta:
    run: ../tools/fastq_to_fasta.cwl
    in:
      fastq: trim_quality_control/reads1_trimmed
    out: [ fasta ]

  clean_fasta_headers:
    run: ../tools/clean_fasta_headers.cwl
    in:
      sequences: convert_trimmed-reads_to_fasta/fasta
    out: [ sequences_with_cleaned_headers ]


$namespaces:
 edam: http://edamontology.org/
 s: http://schema.org/
$schemas:
 - http://edamontology.org/EDAM_1.16.owl
 - https://schema.org/docs/schema_org_rdfa.html

s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"

cwltool: Local (Linux, OS X, Windows)

Arvados: AWS, GCP, Azure, Slurm

Toil: AWS, Azure, GCP, Grid Engine, LSF, Mesos, OpenStack, Slurm, PBS/Torque

Rabix Bunny: Local(Linux, OS X), GA4GH TES

cwl-tes: Local, GCP, AWS, HTCondor, Grid Engine, PBS/Torque, Slurm

CWL-Airflow: Linux, OS X

REANA: Kubernetes, CERN OpenStack

cromwell: local, HPC, Google, HtCondor

CWLEXEC: IBM Spectrum LSF

XENON: any Xenon backend: local, ssh, SLURM, Torque, Grid Engine

Which CWL engine runs where?

Containers

Over 13000 CWL Descriptions on GitHub
(of which 3,865 workflows)

 

Repositories

Sharing computational analyses

https://view.commonwl.org/workflows

Data repositories

Selecting a repository

Provenance

Who ran it?

When did it run?

Where did it run?

What workflow ran?

Which tool versions?

What data was created?

 

Copyright © 2013 W3C® (MIT, ERCIM, Keio, Beihang), All Rights Reserved. W3C liability, trademark and document use rules apply.

PROV Model Primer

W3C Working Group Note 30 April 2013

Khan et al,
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
Submitted to GigaScience
https://doi.org/10.5281/zenodo.1966881

$ cwlprov --help
usage: cwlprov [-h] [--version] [--directory DIRECTORY] [--relative]
            [--absolute] [--output OUTPUT] [--verbose] [--quiet] [--hints]
            [--no-hints]
            {validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
            ...

cwlprov explores Research Objects containing provenance of Common Workflow
Language executions. <https://w3id.org/cwl/prov/>

commands:
{validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
    validate            Validate the CWLProv Research Object
    info                show research object Metadata
    who                 show Who ran the workflow
    prov                export workflow execution Provenance in PROV format
    inputs              list workflow/step Input files/values
    outputs             list workflow/step Output files/values
    run                 show workflow Execution log
    runs                List all workflow executions in RO
    rerun               Rerun a workflow or step
    derived             list what was Derived from a data item, based on
                        activity usage/generation
    runtimes            calculate average step execution Runtimes

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

Research Object

Who is using Research Objects?

https://osf.io/h59uh/

doi.org/10.1371/journal.pbio.3000099

 

P2791

2019-03-11 Sharing reproducible computational analyses

By Stian Soiland-Reyes

2019-03-11 Sharing reproducible computational analyses

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