v0.29.0

• Removed a lot of unused files in the repo.
• Instead of querying Cromwell during the submission, pipeline-tools is getting the versions of the pipelines directly from the WDL files.

v0.28.2

Add cromwell maxRetries runtime parameter to the submit wdl tasks "get_metadata" and "stage_files"

v0.28.1

• Update to use hca CLI version v4.4.0, which fixes changed the mechanism to throw exceptions when an error occurs.

v0.28.0

• Retry HTTP requests with a 409 status code

v0.27.0

• Use CaaS Prod within the Cromwell-metadata docker image, which is used in Submit WDL task.

v0.26.0

Changes

• Optimus works with latest schema and bundle structure
• Adding md5 checksums to results bundle metadata is optional and turned off by default due to HumanCellAtlas/secondary-analysis#287

v0.25.0

Changes

• [Breaking Change] Update to the latest HCA metadata schema:

  • analysis_json now is split into analysis_process and analysis_protocol, the former varies between runs, while the latter remains almost static given a specific version of the analysis pipeline.
  • Link analysis_protocol to analysis_process during the process of creating the submission envelope.
  • Update the testing data.
  • Update both SmartSeq2 and Optimus adapter workflows accordingly.

• [Breaking Change] Update to the latest Bundle structure proposed by Ingest service, which breaks metadata file into smaller separate files.

• [Breaking Change] Migrate to use the centralized metadata-api to prepare inputs for analysis pipelines. Leaving the part for preparing inputs for Optimus pipeline broken intentionally.

• [Breaking Change] Migrate to Python3 and drop support for Python 2.x, update the dockerfile accordingly.

• Migrate from unittest to pytest throughout the code base, update most of the testing cases, introduces a set of new testing fixtures.

• Remove the redundant 10x adapter workflows.

• Update the cromwell-metadata docker image.

v0.24.0

• Add "schema_url" parameter to configure with HCA metadata schemas to use when constructing the analysis JSON

v0.23.0

In this release

• Respect Retry-After headers when following redirects (#61)
• Submit real md5 checksums along with pipeline outputs (#59)
• Make submission tasks idempotent (#58)

v0.22.0

In this release

• Update to v4 hca cli
• Restrict dependencies to a single major version
• Add logging related to http request retries
• Fix bug in parsing analysis workflow id from Cromwell metadata