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-workflowsor 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]
...
