The Wayback Machine - https://web.archive.org/web/20200619105305/https://github.com/broadinstitute/cromwell
Skip to content

/ cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
workflow-execution workflow cloud hpc bioinformatics executor scala docker ga4gh containers wdl workflow-description-language cwl common-workflow-language application
Scala Java wdl Common Workflow Language Shell Python Other
  1. Scala 69.5%
  2. Java 10.8%
  3. wdl 8.6%
  4. Common Workflow Language 8.3%
  5. Shell 1.7%
  6. Python 0.6%
  7. Other 0.5%
Branch: develop
Find file
Clone or download

Clone with HTTPS

Use Git or checkout with SVN using the web URL.

Open in Desktop Download ZIP

Latest commit

@markjschreiber
markjschreiber AWS backend reworked (Issue #5004) (#5468)
Latest commit 88a35b1 Jun 18, 2020

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github Update issue template to point to Jira (#4995) May 24, 2019
CromIAM/src Fix Swagger auth (#5383) [BA-6185] Jan 27, 2020
backend Allow call caching based on singularity paths [BA-6440] (#5543) Jun 16, 2020
centaur Allow call caching based on singularity paths [BA-6440] (#5543) Jun 16, 2020
centaurCwlRunner/src Restored support for Genomics v2alpha1, updated Centaur tests [BA-6057] Feb 3, 2020
cloud-nio Develop Edition: Dos2Drs (#5163) Sep 16, 2019
cloudSupport/src Unify the approach to credential validation Oct 24, 2019
codegen_java Swagger CodeGen for WaaS [BA-5746] (#5038) Jun 27, 2019
common/src Add labels to subworkflows during Carbonite thawing [BA-5875] (#5223) Oct 18, 2019
core/src Limit the number of failed cache hit copy attempts [BA-6430] (#5514) May 29, 2020
cromwell-drs-localizer/src/main/scala/drs/localizer Develop Edition: Dos2Drs (#5163) Sep 16, 2019
cromwell.example.backends Allow call caching based on singularity paths [BA-6440] (#5543) Jun 16, 2020
cromwellApiClient/src Test labels addition, update, and subsequent retrieval after archival [… Mar 12, 2020
cwl/src remove CWL Json encoders (#5212) Oct 4, 2019
database Cromwell should prevent itself from dying on attempt to read too larg… May 20, 2020
docker Less centaur/carbonite logging for travis's sake [BA-6114] (#5275) Nov 15, 2019
dockerHashing/src .trim() Docker image names to avoid pathological re behavior [BA-6478] ( Jun 17, 2020
docs Allow call caching based on singularity paths [BA-6440] (#5543) Jun 16, 2020
engine/src Call caching limit tests and metrics [BA-6457] (#5534) Jun 8, 2020
filesystems AWS backend reworked (Issue #5004) (#5468) Jun 18, 2020
hybridCarboniteMetadataService/src Do not log programmer error when Carboniting failed with `TooLargeToA… Jun 5, 2020
languageFactories Fix occasional errors in WomtoolServiceInCromwellActorSpec due to new… ( Apr 2, 2020
perf/src/main Update cats to 2.0 (#5207) Oct 3, 2019
processes More info on the publish WDL [BA-6284] (#5433) Mar 2, 2020
project AWS backend reworked (Issue #5004) (#5468) Jun 18, 2020
publish Publish WDL using a GitHub token & Docker May 24, 2019
scripts Update Dockerfile to newer OpenJDK to sidestep expired cert [BA-6466] (… Jun 3, 2020
server/src Call caching limit tests and metrics [BA-6457] (#5534) Jun 8, 2020
services/src Fixed error on attempt to get metadata for workflow with archived sta… Jun 11, 2020
src/ci AWS backend reworked (Issue #5004) (#5468) Jun 18, 2020
supportedBackends AWS backend reworked (Issue #5004) (#5468) Jun 18, 2020
wdl WDL 2.0: min and max functions [BA-6158] (#5338) Feb 5, 2020
wes2cromwell/src/main Centaur test carbonite process [BA-6052] (#5237) Nov 6, 2019
wom/src Fix bug where size for a relative input does not work on the shared f… May 21, 2020
womtool Updated `broad-references` bucket name to `gcp-public-data--broad-ref… Feb 11, 2020
.dockerignore move cromwell Feb 25, 2018
.gitattributes move cromwell Feb 25, 2018
.gitignore Digester for Workflow metadata for performance comparison (part I) [B… May 14, 2020
.sbtopts Don't request more mem than most IntelliJ's need for sbt-import. Dec 11, 2018
.travis.yml Unit testing for performance comparison python scripts [BA-6392] (#5502) May 11, 2020
AUTHORS move cromwell Feb 25, 2018
CHANGELOG.md Document the usage of a singularity cache. Encourage users to use the… Jun 3, 2020
CITATION.md Create CITATION.md (#4890) Apr 24, 2019
CONTRIBUTING.md Contributing formatting (#4937) May 9, 2019
LICENSE-ASL-2.0 move cromwell Feb 25, 2018
LICENSE.txt move cromwell Feb 25, 2018
README.md docs: add Ecosystem page (#5427) Feb 25, 2020
build.sbt Add xxh64 and fingerprint call-caching strategies to address shortcom… Apr 27, 2020
codecov.yml No one was paying attention to test coverage in slack, so removing th… Jun 18, 2020
minnie-kenny.gitconfig Added a draft version of minnie-kenny.sh BA-5810 (#5156) Sep 10, 2019
minnie-kenny.sh Update minnie-kenny.sh to run with Jenkins' old git (#5169) Sep 11, 2019
mkdocs.yml Allow non-call-cached tasks (#5426) Feb 25, 2020

README.md

Build Status codecov

Welcome to Cromwell

Cromwell is a Workflow Management System geared towards scientific workflows. Cromwell is open sourced under the BSD 3-Clause license.

The Cromwell documentation has a new home, click here to check it out!

First time to Cromwell? Get started with Tutorials!

Thinking about contributing to Cromwell? Get started by reading our Contributor Guide.

Cromwell has a growing ecosystem of community-backed projects to make your experience even better! Check out our Ecosystem page to learn more.

Issue tracking is now on JIRA

Need to file an issue? Head over to our JIRA. You can sign in with any Google account.

As of May 2019, we are in the process of migrating all issues from Github to JIRA. At a later date to be announced, submitting new Github issues will be disabled.

Jamie, the Cromwell pig

You can’t perform that action at this time.