<commit_before>[![Build Status](https://travis-ci.org/broadinstitute/cromwell.svg?branch=develop)](https://travis-ci.org/broadinstitute/cromwell?branch=develop)
[![Coverage Status](https://coveralls.io/repos/broadinstitute/cromwell/badge.svg?branch=develop)](https://coveralls.io/r/broadinstitute/cromwell?branch=develop)
[![Stories in Ready](https://badge.waffle.io/broadinstitute/cromwell.svg?label=ready&title=Ready)](http://waffle.io/broadinstitute/cromwell)
[![Join the chat at https://gitter.im/broadinstitute/cromwell](https://badges.gitter.im/broadinstitute/cromwell.svg)](https://gitter.im/broadinstitute/cromwell?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)

Cromwell
========

A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management_system) geared towards [scientific workflows](https://en.wikipedia.org/wiki/Scientific_workflow_system). Cromwell is open sourced under the BSD 3-Clause license.

<!---toc start-->

* [How To Reach Us](#how-to-reach-us)
  * [Gitter](#gitter)
  * [Mailing List](#mailing-list)
* [Requirements](#requirements)
* [Building](#building)
* [Installing](#installing)
* [Command Line Usage](#command-line-usage)
  * [run](#run)
  * [server](#server)
* [Getting Started with WDL](#getting-started-with-wdl)
* [Configuring Cromwell](#configuring-cromwell)
  * [Database](#database)
  * [SIGINT abort handler](#sigint-abort-handler)
* [Backends](#backends)
  * [Backend Filesystems](#backend-filesystems)
    * [Shared Local Filesystem](#shared-local-filesystem)
    * [Google Cloud Storage Filesystem](#google-cloud-storage-filesystem)
  * [Local Backend](#local-backend)
  * [Sun GridEngine Backend](#sun-gridengine-backend)
  * [Google JES Backend](#google-jes-backend)
    * [Configuring Google Project](#configuring-google-project)
    * [Configuring Authentication](#configuring-authentication)
      * [Application Default Credentials](#application-default-credentials)
      * [Service Account](#service-account)
    * [Data Localization](#data-localization)
    * [Docker](#docker)
    * [Monitoring](#monitoring)
* [Runtime Attributes](#runtime-attributes)
  * [continueOnReturnCode](#continueonreturncode)
  * [cpu](#cpu)
  * [disks](#disks)
  * [zones](#zones)
  * [docker](#docker)
  * [failOnStderr](#failonstderr)
  * [memory](#memory)
  * [preemptible](#preemptible)
* [Logging](#logging)
* [Workflow Options](#workflow-options)
* [Call Caching](#call-caching)
* [REST API](#rest-api)
  * [REST API Versions](#rest-api-versions)
  * [POST /api/workflows/:version](#post-apiworkflowsversion)
  * [POST /api/workflows/:version/validate](#post-apiworkflowsversionvalidate)
  * [GET /api/workflows/:version/query](#get-apiworkflowsversionquery)
  * [GET /api/workflows/:version/:id/status](#get-apiworkflowsversionidstatus)
  * [GET /api/workflows/:version/:id/outputs](#get-apiworkflowsversionidoutputs)
  * [GET /api/workflows/:version/:id/timing](#get-apiworkflowsversionidtiming)
  * [GET /api/workflows/:version/:id/outputs/:call](#get-apiworkflowsversionidoutputscall)
  * [GET /api/workflows/:version/:id/logs/:call](#get-apiworkflowsversionidlogscall)
  * [GET /api/workflows/:version/:id/logs](#get-apiworkflowsversionidlogs)
  * [GET /api/workflows/:version/:id/metadata](#get-apiworkflowsversionidmetadata)
  * [POST /api/workflows/:version/:id/abort](#post-apiworkflowsversionidabort)
  * [POST /api/workflows/:version/:id/call-caching](#post-apiworkflowsversionidcall-caching)
  * [POST /api/workflows/:version/:id/call-caching/:call](#post-apiworkflowsversionidcall-cachingcall)
  * [Error handling](#error-handling)
* [Developer](#developer)
  * [Generating table of contents on Markdown files](#generating-table-of-contents-on-markdown-files)
  * [Generating and Hosting ScalaDoc](#generating-and-hosting-scaladoc)

<!---toc end-->

# How To Reach Us

## Gitter
There is a [gitter channel](https://gitter.im/broadinstitute/cromwell) where people can discuss Cromwell and related topics with both the developers and user community.

## Mailing List
The [Cromwell Mailing List](https://groups.google.com/a/broadinstitute.org/forum/?hl=en#!forum/cromwell) is <EMAIL>.

If you have any questions, suggestions or support issues please send them to this list. To subscribe you can either join via the link above or send an email to <EMAIL>.

# Requirements

The following is the toolchain used for development of Cromwell.  Other versions may work, but these are recommended.

* [Scala 2.11.7](http://www.scala-lang.org/news/2.11.7/)
* [SBT 0.13.8](https://github.com/sbt/sbt/releases/tag/v0.13.8)
* [Java 8](http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html)

# Building
<commit_msg>update readme to reflect website<commit_after>[![Build Status](https://travis-ci.org/broadinstitute/cromwell.svg?branch=develop)](https://travis-ci.org/broadinstitute/cromwell?branch=develop)
[![Coverage Status](https://coveralls.io/repos/broadinstitute/cromwell/badge.svg?branch=develop)](https://coveralls.io/r/broadinstitute/cromwell?branch=develop)
[![Stories in Ready](https://badge.waffle.io/broadinstitute/cromwell.svg?label=ready&title=Ready)](http://waffle.io/broadinstitute/cromwell)
[![Join the chat at https://gitter.im/broadinstitute/cromwell](https://badges.gitter.im/broadinstitute/cromwell.svg)](https://gitter.im/broadinstitute/cromwell?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)

Cromwell
========

A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management_system) geared towards [scientific workflows](https://en.wikipedia.org/wiki/Scientific_workflow_system). Cromwell is open sourced under the BSD 3-Clause license.

<!---toc start-->

* [Getting Help](#getting-help)
  * [Website and User Guide](#website-and-user-guide)
  * [Support Forum](#support-forum)
  * [Gitter](#gitter)
* [Requirements](#requirements)
* [Building](#building)
* [Installing](#installing)
* [Command Line Usage](#command-line-usage)
  * [run](#run)
  * [server](#server)
* [Getting Started with WDL](#getting-started-with-wdl)
* [Configuring Cromwell](#configuring-cromwell)
  * [Database](#database)
  * [SIGINT abort handler](#sigint-abort-handler)
* [Backends](#backends)
  * [Backend Filesystems](#backend-filesystems)
    * [Shared Local Filesystem](#shared-local-filesystem)
    * [Google Cloud Storage Filesystem](#google-cloud-storage-filesystem)
  * [Local Backend](#local-backend)
  * [Sun GridEngine Backend](#sun-gridengine-backend)
  * [Google JES Backend](#google-jes-backend)
    * [Configuring Google Project](#configuring-google-project)
    * [Configuring Authentication](#configuring-authentication)
      * [Application Default Credentials](#application-default-credentials)
      * [Service Account](#service-account)
    * [Data Localization](#data-localization)
    * [Docker](#docker)
    * [Monitoring](#monitoring)
* [Runtime Attributes](#runtime-attributes)
  * [continueOnReturnCode](#continueonreturncode)
  * [cpu](#cpu)
  * [disks](#disks)
  * [zones](#zones)
  * [docker](#docker)
  * [failOnStderr](#failonstderr)
  * [memory](#memory)
  * [preemptible](#preemptible)
* [Logging](#logging)
* [Workflow Options](#workflow-options)
* [Call Caching](#call-caching)
* [REST API](#rest-api)
  * [REST API Versions](#rest-api-versions)
  * [POST /api/workflows/:version](#post-apiworkflowsversion)
  * [POST /api/workflows/:version/validate](#post-apiworkflowsversionvalidate)
  * [GET /api/workflows/:version/query](#get-apiworkflowsversionquery)
  * [GET /api/workflows/:version/:id/status](#get-apiworkflowsversionidstatus)
  * [GET /api/workflows/:version/:id/outputs](#get-apiworkflowsversionidoutputs)
  * [GET /api/workflows/:version/:id/timing](#get-apiworkflowsversionidtiming)
  * [GET /api/workflows/:version/:id/outputs/:call](#get-apiworkflowsversionidoutputscall)
  * [GET /api/workflows/:version/:id/logs/:call](#get-apiworkflowsversionidlogscall)
  * [GET /api/workflows/:version/:id/logs](#get-apiworkflowsversionidlogs)
  * [GET /api/workflows/:version/:id/metadata](#get-apiworkflowsversionidmetadata)
  * [POST /api/workflows/:version/:id/abort](#post-apiworkflowsversionidabort)
  * [POST /api/workflows/:version/:id/call-caching](#post-apiworkflowsversionidcall-caching)
  * [POST /api/workflows/:version/:id/call-caching/:call](#post-apiworkflowsversionidcall-cachingcall)
  * [Error handling](#error-handling)
* [Developer](#developer)
  * [Generating table of contents on Markdown files](#generating-table-of-contents-on-markdown-files)
  * [Generating and Hosting ScalaDoc](#generating-and-hosting-scaladoc)

<!---toc end-->

# Getting Help

## Website and User Guide

The [WDL website](https://software.broadinstitute.org/wdl/) is the best place to go for more information on both WDL and Cromwell. In particular new users should check out the [user guide](https://software.broadinstitute.org/wdl/userguide/) which has many tutorials, examples and other bits to get you started.

## Support Forum

If you have questions that aren't covered by the website you can ask them in the [support forum](http://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).

## Gitter
There is a [Cromwell gitter channel](https://gitter.im/broadinstitute/cromwell) where people can discuss Cromwell and related topics with both the developers and user community.

# Requirements

The following is the toolchain used for development of Cromwell.  Other versions may work, but these are recommended.

* [Scala 2.11.7](http://www.scala-lang.org/news/2.11.7/)
* [SBT 0.13.8](https://github.com/sbt/sbt/releases/tag/v0.13.8)
* [Java 8](http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html)

# Building

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{'dir': 'git-commits-cleaned', 'id': '2029165', 'n_tokens_mistral': 3550, 'n_tokens_neox': 3354, 'n_words': 517}