Metadata-Version: 2.1
Name: biowardrobe-cwl-workflows
Version: 1.0.20181213214400
Summary: Wrapped BioWardrobe's CWL files
Home-page: https://github.com/datirium/workflows
Author: Datirium, LLC
Author-email: support@datirium.com
License: UNKNOWN
Download-URL: https://github.com/datirium/workflows
Description: [![Build Status](https://travis-ci.org/datirium/workflows.svg?branch=master)](https://travis-ci.org/datirium/workflows)
        # Workflows
        CWL workflows for [BioWardrobe](https://biowardrobe.com/) 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 
        
        ```sh
        pip3 install biowardrobe-cwl-workflows
        ```
        or from sources
        ```sh
        git clone https://github.com/datirium/workflows
        pip3 install .
        ```
        
        ## Usage
        
        ```python
        from biowardrobe_cwl_workflows import available
        _path_to_workflow=available(workflow='chipseq-se.cwl')
        ```
        
        ## Extra features in CWL
        
        ### Metadata & Upstreams
        ```yaml
        '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:
        
        ```yaml
        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
        
        ```yaml
        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]
          ...
        ```
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: OS Independent
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Operating System :: Microsoft :: Windows :: Windows 8.1
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Description-Content-Type: text/markdown
