Metadata-Version: 2.1
Name: janis-pipelines.runner
Version: 0.1.0
Summary: Easier way to run workflows, configurable across environments
Home-page: UNKNOWN
Author: Michael Franklin
Author-email: michael.franklin@petermac.org
License: MIT
Description: # Welcome to Janis-Runner
        
        This project aims to make the processing of running workflows easier, when your workflow 
        is built with [Janis](https://github.com/PMCC-BioinformaticsCore/janis).
        
        ## Quick start
        
        ```bash
        pip3 install janis_runner 
        ```
        
        ## How to run a workflow
        
        You can either run a workflow from the command line, or there are a few exposed methods.
        
        ### Command Line
        
        ```bash
        janis run --environment local /path/to/myworkflow.py
        ```
        
        Extra parameters:
        
        > Put help guide here
        
        
        ## Environments
        
        This is the first step. Can we take a workflow written in CWL or WDL, Spin up an instance of 
        [Cromwell](https://github.com/broadinstitute/cromwell), run the workflow with any required tools and give back the user the result.
        
        This would greatly simplify the knowledge required to get a pipeline running, something like:
        
        ```bash
        shepherd run workflow.cwl --inputs workflow-inputs.yml --tools tools.zip --env pmac --output-dir .
        ``` 
        
        #### General structure
        
        1. Take input files
        2. Determine environment
            1. If it's PMAC, might need to check for docker / singularity / modules and generate correct config
        3. Start up Cromwell (in server mode)
        4. Schedule job
        5. Monitor job process
            1. Return any errors that may occur
            2. Give user running feedback
        6. Collect output files
        7. Shutdown cromwell server
Keywords: janis,workflows,enginerunner
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Environment :: Console
Description-Content-Type: text/markdown
