2.1.1

Version Bump (#275)

2.1.0

Additions

• PR265 Added validate command: When invoked performs WDL workflow validation using Cromwell's womtool API and miniwdl. It checks the syntax and type errors in the provided WDL and its associated input JSON file, and it can also optionally handle local imports via miniwdl. If successful, it prints "Validation successful"; otherwise, it prints "Validation failed."
• PR268 Flatten and submit nested WDLs: This update addresses a common issue regarding path resolution in nested directory structures when working with WDLs. It introduces a new feature to the submit command, which automatically detects relative imports in workflows, creates a temporary directory, and rewrites WDLs with adjusted imports, making it easier to work with dependencies both within and outside of Terra.

Bug Fixes

• PR256 Fix to have the version command print the version
• PR271 Fix to have metadata and slim-metadata print machine-readable json

2.0.0

We are excited to announce the release of Cromshell 2! This new version of Cromshell brings a number of improvements and new features to the Cromwell job submission experience.

Here are some of the key highlights of Cromshell 2:

• A completely rebuilt codebase in Python, which brings improved reliability, performance, and modularity to the tool.
• Automatic zipping of workflow dependencies when submitting a workflow.
• Integration and unit tests to ensure Cromshell remains a reliable and robust tool.
• Multiple installation options: Cromshell 2 can be installed from source, via Homebrew, or from PyPI.
• A modular architecture that makes adding new functionalities and commands easier.
• Developer documentation that provides guidance on how to add new features and commands to the tool.

The original Cromshell shell script is still available in the legacy_cromshell folder and in the cromshell1 branch of this repository.It is no longer maintained, but is still available for use. The original Cromshell contains some commands not yet available in Cromshell2,such as fetch-logs, fetch-all, notify, and cleanup. These commands will be added to Cromshell2 in the future.

2.0.0.beta.1

Beta release of Cromshell2

Added commands:

• alias - Label the given workflow ID with the given alias
• counts - Get the summarized status of all jobs in the workflow (same as execution-status-count)
• list - Display a list of jobs submitted through cromshell
• logs - List the log files produced by a workflow.
• timing - Open the timing diagram in a browser.
• update-server - Change the Cromwell server to which new jobs will be submitted.

Added features

• Developer documentation - Step-by-step instructions on adding new commands and their tests to cromshell. #195
• Automatically zip dependency files when submitting a workflow. #214
• Support for users running Cromshell against Cromwell server in Terra workspace. Contributed by the Cromwell team. #208

0.5.3

Bug fix release.
ad30776 Fixes cost and detailed cost queries for new billing setup as of 2022 Aug 11 (#219)
e119c23 Add note about cromshell 2 alpha to readme (#211)
bb9a1b1 Fixing issue where tasks would be incorrectly labeled as failed. (#190)

2-alpha.1

Alpha release of Cromshell2

This is a rewrite in python which is currently not feature complete with the original. You can view it and contribute in the cromshell_2.0 branch.

Contains the following commands:

• abort - Abort a running workflow.
• metadata - Get the full metadata of a workflow.
• slim-metadata - Get a subset of the workflow metadata.
• status - Check the status of a Cromwell job UUID
• submit - Submit a workflow and arguments to the Cromwell Server

Please see the Please see the README for python installation instructions.

0.5.2

You can now add header parameters to your curl requests using the new CROMSHELL_HEADER environment variable. This is useful for cromwell servers that add an authentication layer based on oath headers.

c619d26 Update README.md (#178)
f0f8033 Add curl headers (#175)
cbcb0e8 Add note about bq init to README (#170)

0.5.1

Bugfixes!
d047632 Fix timing command #167 (#168)
c6389c5 Updating wait time for cost and cost-detailed from 8h to 24h (#166)

0.5.0

New Feature: Workflow costs.

• New commands cost and cost-detailed which lookup the cost of completed workflows and show the total or per-task costs.
  These require a new config file ~/.cromshell/gcp_bq_cost_table.config which includes the name of your google cloud costs BigQuery table.

4df19a6 Readme and completions fixups (#165)
90a5f53 Adding zsh completions for cost commands (#164)
3e0586f Added cost commands. (#163)
69d2e4a Removing another temporary file from notify daemon. (#162)

0.4.4

Added a new update-server command to rerun the server initialization dialog.

4787986 Add the sub-command "update-server" (#140)
c2e8c7b explicitly prepend http to server address when IP address is used instead of an url (#145)
c7ea883 Fixing issue with aliases and GNU grep. (#136)