Workflows

CWL workflows for BioWardrobe project. This package includes all the original BioWardrobe's pipelines, simplifies import for biowardrobe-airflow-analysis. It also includes extra pipelines for new project SciDAP.

Install

pip3 install biowardrobe-cwl-workflows

or from sources

git clone https://github.com/datirium/workflows
pip3 install .

Usage

from biowardrobe_cwl_workflows import available
_path_to_workflow=available(workflow='chipseq-se.cwl')

Extra features in CWL

Metadata & Upstreams

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

'sd:upstream':
  genome_indices: "genome-indices.cwl"
  control_file: "chipseq-se.cwl"

To enable users 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 workflows where inputs field just used for constructing and storing the input object.

To simplify selection of already analyzed common data ’sd:upstream’ were introduced. It defines the upstream workflows of the process. The process is ready to run when upstream output data is available.

Example of extra input fields 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 #"
  description:
    type: string?
    'sd:type': 'text'
    label: "Description"

outputs: []
steps: []

CWL VisualPlugins for output data

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]
  ...