broadinstitute/cromwell 85 on GitHub

85 Release Notes

Migration of PKs to BIGINT

The PK of below tables will be migrated from INT to BIGINT. Also, since ROOT_WORKFLOW_ID in SUB_WORKFLOW_STORE_ENTRY is a FK to WORKFLOW_STORE_ENTRY_ID in WORKFLOW_STORE_ENTRY
it is also being migrated from INT to BIGINT.

DOCKER_HASH_STORE_ENTRY
WORKFLOW_STORE_ENTRY
SUB_WORKFLOW_STORE_ENTRY

Improvement to "retry with more memory" behavior

Cromwell will now retry a task with more memory after it fails with return code 137, provided all
the other requirements for retrying with more memory are met.

DRS Improvements

Support for invoking `CromwellDRSLocalizer` with manifest file

CromwellDRSLocalizer can now handle multiple file localizations in a single invocation. Users can provide a
manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in
sequence, with the program exiting if any fail.

java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file.txt

The previous method of passing in a single DRS file and container destination using positional arguments is still
supported.

Improvement to DRS localization in GCP papiv2beta backend

All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
failures observed when attempting to localize a large number of DRS files.

Allow list for HTTP WDL resolution

Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported.
Default behavior is unchanged (Cromwell attempts to resolve WDL files from any URI). Example configuration:

languages {
  WDL {
    http-allow-list {
      enabled: true
      allowed-http-hosts: [
        "my.wdl.repo.org",
        "raw.githubusercontent.com"
      ]
    }
  }
}

CWL implementation removed

This release removes the cwl top-level artifact. Some nonfunctional references may remain, and will be addressed over time.

For more information, see the Cromwell 79 release notes.

TES Improvments

Tes system errors are are now reported in Cromwell execution logs when the TES backend returns a task error.
Cromwell now attempts to translate disks attributes written for GCP into valid disk attributes for TES. For information on supported conversions, refer to the TES documentation.

Bug Fixes

Reference disks are only mounted if configured in the workflow options.
Recent docker images of Ubuntu use a new manifest format, ensure that these newer image versions can be pulled from Docker Registry without issue.
When converting ValueStore objects to strings for logging, we truncate long values to limit memory usage.

Security Patching

Updates to dependencies to fix security vulnerabilities.