{ "info": { "author": "Datirium, LLC", "author_email": "support@datirium.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Environment :: Other Environment", "Intended Audience :: Developers", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Natural Language :: English", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: Microsoft :: Windows :: Windows 10", "Operating System :: Microsoft :: Windows :: Windows 8.1", "Operating System :: OS Independent", "Operating System :: POSIX", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Scientific/Engineering :: Medical Science Apps." ], "description": "[![Build Status](https://travis-ci.org/datirium/workflows.svg?branch=master)](https://travis-ci.org/datirium/workflows)\n# Workflows\nCWL workflows for [BioWardrobe](https://biowardrobe.com/) project. This package includes \n all the original BioWardrobe's pipelines, simplifies import \nfor biowardrobe-airflow-analysis. It also includes extra pipelines for new project SciDAP.\n\n## Install \n\n```sh\npip3 install biowardrobe-cwl-workflows\n```\nor from sources\n```sh\ngit clone https://github.com/datirium/workflows\npip3 install .\n```\n\n## Usage\n\n```python\nfrom biowardrobe_cwl_workflows import available\n_path_to_workflow=available(workflow='chipseq-se.cwl')\n```\n\n## Extra features in CWL\n\n### Metadata & Upstreams\n```yaml\n'sd:metadata':\n - \"../metadata/chipseq-header.cwl\"\n\n'sd:upstream':\n genome_indices: \"genome-indices.cwl\"\n control_file: \"chipseq-se.cwl\"\n\n```\n\nTo 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. \n\n\nTo simplify selection of already analyzed common data ```\u2019sd:upstream\u2019``` were introduced. It defines the upstream workflows of the process. The process is ready to run when upstream output data is available. \n\n\n##### Example of extra input fields for user interface:\n\n```yaml\ncwlVersion: v1.0\nclass: Workflow\n\ninputs:\n cells:\n type: string\n label: \"Cells\"\n sd:preview:\n position: 1\n conditions:\n type: string\n label: \"Conditions\"\n sd:preview:\n position: 3\n alias:\n type: string\n label: \"Experiment short name/Alias\"\n sd:preview:\n position: 2\n catalog:\n type: string?\n label: \"Catalog #\"\n description:\n type: string?\n 'sd:type': 'text'\n label: \"Description\"\n\noutputs: []\nsteps: []\n\n```\n\n### CWL VisualPlugins for output data\n\n```yaml\noutputs:\n ...\n fastx_statistics:\n type: File\n label: \"FASTQ statistics\"\n format: \"http://edamontology.org/format_2330\"\n doc: \"fastx_quality_stats generated FASTQ file quality statistics file\"\n outputSource: fastx_quality_stats/statistics_file\n 'sd:visualPlugins':\n - line:\n Title: 'Base frequency plot'\n xAxisTitle: 'Nucleotide position'\n yAxisTitle: 'Frequency'\n colors: [\"#b3de69\", \"#99c0db\", \"#fb8072\", \"#fdc381\", \"#888888\"]\n data: [$12, $13, $14, $15, $16]\n ...\n```", "description_content_type": "text/markdown", "docs_url": null, "download_url": "https://github.com/datirium/workflows", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/datirium/workflows", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "biowardrobe-cwl-workflows", "package_url": "https://pypi.org/project/biowardrobe-cwl-workflows/", "platform": "", "project_url": "https://pypi.org/project/biowardrobe-cwl-workflows/", "project_urls": { "Download": "https://github.com/datirium/workflows", "Homepage": "https://github.com/datirium/workflows" }, "release_url": "https://pypi.org/project/biowardrobe-cwl-workflows/1.0.20181213214400/", "requires_dist": null, "requires_python": "", "summary": "Wrapped BioWardrobe's CWL files", "version": "1.0.20181213214400" }, 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