{ "info": { "author": "Seven Bridges Genomics Inc.", "author_email": "filip.tubic@sbgenomics.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Developers", "License :: Other/Proprietary License", "Natural Language :: English", "Operating System :: POSIX", "Programming Language :: Python :: 3" ], "description": "SevenBridges CWL \n===========================\n\n# Table of contents\n1. [Overview](#overview)\n2. [Install](#install)\n3. [Docs](#docs)\n4. [Run tests](#tests)\n5. [Examples](#examples)\n - [Run workflow on a SevenBridges platform](#example1)\n\n## Overview\n\n**SevenBridges CWL** package provides python bindings for \n_Common Workflow Language_. It is intended for developers who want to use \npython code to generate CWL documents. If creating a document through the GUI\nis preferable, then look at the \n[Rabix Composer](https://github.com/rabix/composer).\n\n## Install\n\n### Official releases\nOfficial releases are available via `pip install sevenbridges-cwl` (This is the [pypi entry](https://pypi.org/project/sevenbridges-cwl/) for this project)\n\n### Development versions\nTo obtain unreleased versions: \n\n- `git clone` this repository \n- `cd sevenbridges-cwl && pip install .`\n\nThe `master` branch is for more stable code while `develop` is for cutting edge features being currently worked on\n\n## Docs\n\nComplete documentation can be found [here](https://sevenbridges-cwl.readthedocs.io/en/latest/quickstart.html).\n\nIf you are interested in reviewing this documentation locally, clone this \nrepository, position yourself in the `docs` directory and after installing \n`requirements-dev.txt`, invoke:\n\n```\nmake html\n```\n\n## Run Tests\n\nIn order to run tests clone this repository, position yourself in the root of \nthe cloned project and, after installing `requirements-dev.txt`, invoke: \n```\npytest\n```\n\n## Examples\n\nThe following code will give a brief overview of what this package can offer through \nsimple examples. \n\n**A Complete list of all examples can be found here.**\n\n### Run workflow on a SevenBridges platform\n\n```python\nfrom sbg import cwl\n\n\n# First node\n@cwl.to_tool(\n inputs=dict(x=cwl.String()),\n outputs=dict(out=cwl.Float(required=True)),\n docker='images.sbgenomics.com/filip_tubic/ubuntu1604py'\n)\ndef to_float(x):\n return dict(out=float(x))\n\n\n# Second node\n@cwl.to_tool(\n inputs=dict(x=cwl.Float(), n=cwl.Int()),\n outputs=dict(out=cwl.Float()),\n docker='images.sbgenomics.com/filip_tubic/ubuntu1604py'\n)\ndef times_n(x, n=10):\n return dict(out=x * n)\n\n\nwf = cwl.Workflow()\n\n# create tools\nt1 = to_float()\nt2 = times_n()\n\n# steps\nwf.add_step(t1, expose=['x'])\nwf.add_step(t2, expose=['n', 'out'])\n\n# add connections\nwf.add_connection(f'{t1.id}.out', f'{t2.id}.x')\n\n# Session on a SBG platform\nsession = cwl.Session(profile='')\n\nsession.run('', wf, inputs={'x': '10.2'})\n```", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "", "keywords": "seven bridges cwl common workflow language", "license": "Copyright (c) 2018 Seven Bridges Genomics", "maintainer": "Seven Bridges Genomics Inc.", "maintainer_email": "filip.tubic@sbgenomics.com", "name": "sevenbridges-cwl", "package_url": "https://pypi.org/project/sevenbridges-cwl/", "platform": "POSIX", "project_url": "https://pypi.org/project/sevenbridges-cwl/", "project_urls": null, "release_url": "https://pypi.org/project/sevenbridges-cwl/1.1.3/", "requires_dist": null, "requires_python": "", "summary": "SBG Python library to create CWL tools and workflows", "version": "1.1.3" }, "last_serial": 4520854, "releases": { "1.1.0": [ 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