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Common Workflow Language

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL builds on technologies such as JSON-LD. For data modeling and Docker. Web-based...

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Common Workflow Language | commonwl.org Reviews

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The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL builds on technologies such as JSON-LD. For data modeling and Docker. Web-based...

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2 user guide

3 specification

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5 draft 3

6 citation

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Common Workflow Language | commonwl.org Reviews

https://commonwl.org

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL builds on technologies such as JSON-LD. For data modeling and Docker. Web-based...

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Common Workflow Language Viewer

Common Workflow Language Viewer. This tool visualises and lists the details of a workflow with its inputs, outputs and steps and packages the files involved into a downloadable Research Object Bundle. Zip file with metadata in a manifest), allowing it to be easily viewed and shared. This viewer is currently experimental and may not work for all valid workflows. Workflow from Github URL. Provide a Github link to the workflow here. Don't know what to view? Try these from common-workflow-language/workflows.

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commonwl.org

1

Common Workflow Language Specifications, v1.0

http://www.commonwl.org/v1.0

Common Workflow Language Specifications, v1.0. The CWL specifications are divided up into several documents. Provides a gentle introduction to writing CWL command line tools and workflows. The Command Line Tool Description Specification. Specifies the document schema and execution semantics for wrapping and executing command line tools. The Workflow Description Specification. The Semantic Annotations for Linked Avro Data (SALAD) Specification.

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Common Workflow Language, Draft 2

http://www.commonwl.org/draft-2

Common Workflow Language, Draft 2. Status of This Document. 11 Introduction to draft 2. 13 References to Other Specifications. 25 Extensions and Metadata. 32 Generic execution process. 33 Requirements and hints. 36 Success and failure. 37 Executing CWL documents as scripts. 4 Sample CWL workflow. Common Workflow Language, Draft 2. John Chilton jmchilton@gmail.com. Galaxy Project, Pennsylvania State University. Michael R. Crusoe mcrusoe@msu.edu. Maxim Mikheev mikhmv@biodatomics.com. Status of This Document.

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Common Workflow Language

http://www.commonwl.org/index.html

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL builds on technologies such as JSON-LD. For data modeling and Docker. An open-s...

4

A Gentle Introduction to the Common Workflow Language

http://www.commonwl.org/v1.0/UserGuide.html

A Gentle Introduction to the Common Workflow Language. This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0. Note: This document is a work in progress. Not all features are covered, yet. A Gentle Introduction to the Common Workflow Language. 2 Wrapping Command Line Tools. 22 Essential input parameters. 23 Returning output files. 24 Capturing a tool's standard output stream. With th...

5

Common Workflow Language Specifications, draft-3

http://www.commonwl.org/draft-3

Common Workflow Language Specifications, draft-3. The CWL specifications are divided up into several documents. Provides a gentle introduction to writing CWL command line tools and workflows. The Command Line Tool Description Specification. Specifies the document schema and execution semantics for wrapping and executing command line tools. The Workflow Description Specification. The Semantic Annotations for Linked Avro Data (SALAD) Specification.

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Presentations — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/presentations.html

Common Workflow Language (CWL). Links from the presentation. MIT Bioinformatics Interest Group. About how Common Workflow Language enables interoperability with multiple workflow engines. 3 November 2016): slides. Software engineering seminar about bcbio validation and intergration with Common Workflow Language and Workflow Definition Language (28 September 2016): slides. At the Summer 2016 NGS Data Analysis Course at Harvard Chan School. 11 August 2016): slides. 28 April 2016): slides. Prioritization of...

smallchangebio.wordpress.com

Notes: Bioinformatics Open Source Conference 2016 day 1 morning — Open Data and infectious disease, workflows | Small Change Bioinformatics

https://smallchangebio.wordpress.com/2016/07/08/bosc2016_day1a

Notes: Bio in Docker Symposium 2015 day 2: Docker infrastructure and hackathon. Notes: Bioinformatics Open Source Conference 2016 day 1 afternoon: Standards; Panel on growing communities →. July 8, 2016. Notes: Bioinformatics Open Source Conference 2016 day 1 morning — Open Data and infectious disease, workflows. I’m at the 2016 Bioinformatics Open Source Conference (BOSC). Jennifer Gardy – The open-source outbreak: can data prevent the next pandemic? Awesome work on crowd sourcing problem: EpiCollect.

toil.readthedocs.io

Running a workflow — Toil 3.3.6a1 documentation

http://toil.readthedocs.io/en/releases-3.3.x/running.html

Starting with Python, a Toil workflow can be run with just three steps. Copy and paste the following code block into HelloWorld.py. Prints Hello, world! Now you have run Toil on singleMachine. Default batch system) using the FileStore. Job store. The first positional argument after the. Is the location of the job store, a place where intermediate files are written to. In this example, a folder called jobStore. Will be created where HelloWorld.py. To see a complete list of available options. For a detaile...

toil.readthedocs.io

Installation — Toil 3.3.6a1 documentation

http://toil.readthedocs.io/en/releases-3.3.x/installation.html

Python 2.7.x. To setup a basic Toil installation use. Toil uses setuptools’ extras. Mechanism for dependencies of optional features like support for Mesos or AWS. To install Toil with all bells and whistles use. Pip install toil[aws,mesos,azure,google,encryption,cwl]. Here’s what each extra provides:. Extra provides support for storing workflow state in Amazon AWS. This extra has no native dependencies. Extra stores workflow state in Microsoft Azure Storage. This extra has no native dependencies. Is prob...

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commonwl.org

Common Workflow Language

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL builds on technologies such as JSON-LD. For data modeling and Docker. Web-based...

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