Metadata-Version: 2.1
Name: janis-pipelines
Version: 0.9.2
Summary: Contains classes and helpers to build a workflow, and provide options to convert to CWL / WDL
Home-page: https://github.com/PMCC-BioinformaticsCore/janis
Author: Michael Franklin, Richard Lupat
Author-email: michael.franklin@petermac.org
License: GNU
Description: # Janis (janis-pipelines) (Alpha)
        
        
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        _Janis is a framework creating specialised, simple workflow definitions that are then transpiled to   
        Common Workflow Language or Workflow Definition Language._  
          
        Documentation is hosted here: https://janis.readthedocs.io/
        
        
        ## v0.9.0 release
        
        > v0.9.0 includes backwards incompatible changes, see the [CHANGELOG](https://github.com/PMCC-BioinformaticsCore/janis/blob/master/CHANGELOG.md)
        for more information.
        
          
        ## Introduction  
        
        >| WARNING: this project is work-in-progress and is provided as-is without warranty of any kind. There may be breaking changes committed to this repository without notice. |
        >|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
        
        
        Janis gives you an API to build computational workflows and will generate
        a workflow description in CWL and WDL. By using Janis, you get type-safety,
        portability and reproducibility across all of your execution environments.
        
        
        Janis requires a Python installation > 3.6, and can be installed through PIP 
        ([project page](https://pypi.org/project/janis-pipelines/)):  
          
        ```bash
        # Install janis and the bioinformatics tools
        pip3 install janis-pipelines 
        ```  
          
        You can import Janis into your project with:  
        ```python  
        import janis as j  
        ```
        
        ### Example  
          
        Below we've constructed a simple example that takes a string input, calls the 
        [echo](https://janis.readthedocs.io/en/latest/tools/unix/echo.html) tool and exposes the 
        Echo tool's output as a workflow output.  
          
        ```python  
        import janis as j
        from janis.tools import Echo
        
        w = j.WorkflowBuilder("workflowId")
        
        w.input("inputIdentifier", j.String, default="Hello, World!")
        w.step("stepIdentifier", Echo(inp=w.inputIdentifier))
        w.output("outputIdentifier", source=w.stepIdentifier.out)
        
        # Will print the CWL, input file and relevant tools to the console
        w.translate("cwl", to_disk=False)  # or "wdl"
        ```
        
        We can export a CWL representation to the console using `.translate("cwl")`. By including the 
        `to_disk=True` parameter, we can write this workflow to disk at the current location. 
          
        #### More examples  
        
        - Bioinformatics workflow tutorial: [Aligment](https://janis.readthedocs.io/en/latest/tutorials/tutorial1.html)
        - Simple unix examples: in [`janis/examples`](https://github.com/PMCC-BioinformaticsCore/janis/tree/master/janis/examples).   
        
        - Whole genome germline pipelines: [janis-pipelines repository](https://github.com/PMCC-BioinformaticsCore/janis-pipelines).  
        
        ## About  
          
        > _Further information_: [About](https://janis.readthedocs.io/en/latest/about.html)   
          
        This project was produced as part of the Portable Pipelines Project in partnership with:    
        - [Melbourne Bioinformatics (University of Melbourne) ](https://www.melbournebioinformatics.org.au/)    
        - [Peter MacCallum Cancer Centre](https://www.petermac.org/)    
        - [Walter and Eliza Hall Institute of Medical Research (WEHI) ](https://www.wehi.edu.au/)    
        
        ### References:
        
        Through conference or talks, this project has been referenced by the following titles:
        
        - Walter and Eliza Hall Institute Talk (WEHI) 2019: _Portable Pipelines Project: Developing reproducible bioinformatics pipelines with standardised workflow languages_
        - Bioinformatics Open Source Conference (BOSC) 2019: _Janis: an open source tool to machine generate type-safe CWL and WDL workflows_
        - Victorian Cancer Bioinformatics Symposium (VCBS) 2019: _Developing portable variant calling pipelines with Janis_
        - GIW / ABACBS 2019: _Janis: A Python framework for Portable Pipelines_
        - Australian BioCommons, December 2019: _Portable pipelines: build once and run everywhere with Janis_
          
          
        ## Support  
        
        ## v0.9.0 Backwards Compatability
        
        **NOTE: Version 0.9.0 brings changes to output directories and camel case changes**
        
        - Janis watch will be incompatible with previously run workflows
        - Your configs might break, as previous versions of janis were not cautious about camel case.
        - Your templates might not work with unrecognised keys (try changing them to camel case instead)
        - Changes to BamBai indexes, format is now `.bam.bai`
        
        See the [CHANGELOG](https://github.com/PMCC-BioinformaticsCore/janis/blob/master/CHANGELOG.md)
        for more information.
        
        
        ### Contributions
          
        > _Further information_: [Development](https://janis.readthedocs.io/en/latest/development/)  
          
        To get help with Janis, please ask a question on [Gitter](ttps://gitter.im/janis-pipelines/community) or 
        [raise an issue](https://github.com/PMCC-BioinformaticsCore/janis/issues) on GitHub.
        
        If you find an issue with the tool definitions, please see the relevant issue page:
        
        - [Pipeline-bioinformatics](https://github.com/PMCC-BioinformaticsCore/janis-bioinformatics/issues)
        
        This project is work-in-progress and is still in developments. Although we welcome contributions,
        due to the immature state of this project we recommend raising issues through the
        [Github issues page](https://github.com/PMCC-BioinformaticsCore/janis/issues) for Pipeline related issues.
        
        Information about the project structure and more on contributing can be found within the documentation.
        
Keywords: pipelines,bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Provides-Extra: bioinformatics
