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 with

Metadata

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

Example of 'metadata' template for user interface:

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 allow selection of already analysed data as input for a workflow we organize a graph of separate workflows. To link workflows we use ’sd:upstream’ which defines a list of upstream workflows.

...
'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 or as a table. Keyword 'sd:visualPlugins' enables SciDAP visualization plugins. line, pie, chart, igvbrowser and syncfusiongrid 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
    ...