Bioinformatics Workflows by Datirium LLC

ChIP-Seq, ATAC-Seq, CLIP-Seq, RNA-Seq CWL workflows for use in Scientific Data Analysis Platform (SciDAP) or in BioWardrobe project or standalone with cwltool.

All the original BioWardrobe's pipelines has been rewritten in CWL and new workflows has been added. The repository pulls automatically into SciDAP platform.

Augmented CWL standard for SciDAP

There are 4 additional references that can be given to a workflow for added compatability within SciDAP.

1. Metadata
2. Upstreams
3. Visual Plugins
4. Service Tags

Metadata

To extend user interface (dynamic form) with extra input fields not required by a workflow, the 'sd:metadata' field was introduced. It defines a list of workflow templates where the inputs object is used for constructing and storing extra fields with an original workflow.

Example of 'metadata' template for user interface:

chipseq-header.cwl

cwlVersion: v1.0
class: Workflow

inputs:
  cells:
    type: string
    label: "Cells"
    sd:preview:
        position: 1
  conditions:
    type: string
    label: "Conditions"
    sd:preview:
        position: 3
  alias:
    type: string
    label: "Experiment short name/Alias"
    sd:preview:
        position: 2
  catalog:
    type: string?
    label: "Catalog #"

outputs: []
steps: []

and include file as sd:metadata

'sd:metadata':
    - "../metadata/chipseq-header.cwl"

Upstreams

To extend the SciDAP UI to allow for already analysed data the be selectable as inputs, we organize a graph of separate workflows. To link workflows we use ’sd:upstream’, which defines a list of upstream workflows who's outputs are accible by this workflow.

...
'sd:upstream':
  rnaseq_sample_untreated:
    - "rnaseq-se.cwl"
    - "rnaseq-pe.cwl"
    - "rnaseq-se-dutp.cwl"
    - "rnaseq-pe-dutp.cwl"
    - "rnaseq-se-dutp-mitochondrial.cwl"
    - "rnaseq-pe-dutp-mitochondrial.cwl"
    - "trim-rnaseq-pe.cwl"
    - "trim-rnaseq-se.cwl"
    - "trim-rnaseq-pe-dutp.cwl"
    - "trim-rnaseq-se-dutp.cwl"
  rnaseq_sample_treated:
    - "rnaseq-se.cwl"
    - "rnaseq-pe.cwl"
    - "rnaseq-se-dutp.cwl"
    - "rnaseq-pe-dutp.cwl"
    - "rnaseq-se-dutp-mitochondrial.cwl"
    - "rnaseq-pe-dutp-mitochondrial.cwl"
    - "trim-rnaseq-pe.cwl"
    - "trim-rnaseq-se.cwl"
    - "trim-rnaseq-pe-dutp.cwl"
    - "trim-rnaseq-se-dutp.cwl"

inputs:

  untreated_files:
    type: File[]
    format:
     - "http://edamontology.org/format_3752"
     - "http://edamontology.org/format_3475"
    label: "Untreated input CSV/TSV files"
    doc: "Untreated input CSV/TSV files"
    'sd:upstreamSource': "rnaseq_sample_untreated/rpkm_common_tss"
    'sd:localLabel': true
...

VisualPlugins for an output type file

Usually, workflows' output results (especially files) are provided as download links in web interfaces. With SciDAP visualization plugins, data can be presented as a plot, as a genome browser, as a table, or (in the case of html outputs) to be opened in a new tab. The keyword 'sd:visualPlugins' enables SciDAP visualization plugins. line, pie, chart, igvbrowser, syncfusiongrid, and linkList types are already available in the platform.

outputs:
    ...
    fastx_statistics:
        type: File
        label: "FASTQ statistics"
        format: "http://edamontology.org/format_2330"
        doc: "fastx_quality_stats generated FASTQ file quality statistics file"
        outputSource: fastx_quality_stats/statistics_file
        'sd:visualPlugins':
        - line:
            Title: 'Base frequency plot'
            xAxisTitle: 'Nucleotide position'
            yAxisTitle: 'Frequency'
            colors: ["#b3de69", "#99c0db", "#fb8072", "#fdc381", "#888888"]
            data: [$12, $13, $14, $15, $16]
    ...
    diff_expr_file:
        type: File
        label: "DESeq results, TSV"
        format: "http://edamontology.org/format_3475"
        doc: "DESeq generated list of differentially expressed items grouped by isoforms, genes or common TSS"
        outputSource: deseq/diff_expr_file
        'sd:visualPlugins':
        - syncfusiongrid:
            Title: 'Combined DESeq results'
    ...
    bigwig:
        type: File
        format: "http://edamontology.org/format_3006"
        label: "BigWig file"
        doc: "Generated BigWig file"
        outputSource: bam_to_bigwig/bigwig_file
        'sd:visualPlugins':
        - igvbrowser:
            id: 'igvbrowser'
            type: 'wig'
            name: "BigWig Track"
            height: 120
    ...

Service Tags for workflows

The 'sd:serviceTag'keyword enables new workflows to be added for the creation of:

• samples: uses keyword 'sample'
• analyses: uses keyword 'analysis'
• genelist: uses keywork 'genelist'