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Releases: HumanCellAtlas/lira

v0.11.0

14 Jun 17:55
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  • Add "v6" subscription queries for SmartSeq2 and 10x data
  • Include the fields in notification metadata attachments as workflow labels
  • Set max_cromwell_retries in workflow inputs (defaults to 0)
  • Support HMAC auth for notifications
  • Fix url for registering service account in FireCloud.
  • Move dss_url, ingest_url and Cromwell-as-a-Service params into Lira config for greater flexibility.
  • Hard code kube cluster name to "listener" in lira-deploy Jenkins job to prevent error when multiple clusters are present.
  • Require both user and password when not using Cromwell-as-a-Service
  • Improve instructions for updating a certificate

v0.10.0

04 Jun 14:37
f8adb7c
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  • Improves the scalability and stability of Lira by:
    • Increasing the number of Gunicorn workers.
    • Increasing the timeout and graceful timeout of Gunicorn workers.
    • Replacing the sync workers with gevent workers.
  • Adds the option to include additional metadata in notifications to the utility script when it is making subscriptions.
  • Enables Lira to on hold workflows when it is submitting to Cromwell.

v0.9.1

24 Apr 19:51
3127f2c
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Update kube-deploy script to pass in USE_CAAS parameter when creating the listener-deployment.yaml file.

v0.9.0

24 Apr 19:02
d0dbf45
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Add version endpoint to Lira that includes information about its configuration (e.g. what pipeline versions it is running)

v0.8.0

19 Apr 20:10
6e39af0
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  • Add cromwell-as-a-service support to lira
  • Freeze libraries in requirements.txt

v0.7.0

29 Mar 02:23
d95d64c
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  • Label Feature
    Lira now could add labels to workflows at start time.
  • Minor Fix
    Update thse config ctmpl file to fix the Green Box Integration Test.

v0.6.2

27 Mar 00:39
ee2c015
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  • Dynamically add environment-specific urls for the HCA data storage service and integration service into the lira config
  • Make it possible to use a stub submission wdl

v0.6.1

17 Mar 16:29
5582f6d
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Changes:

  • Fix a bug with cache pool that can possibly break the inputs to Cromwell.

  • Add Elasticsearch queries for both 10x v2 and SmartSeq2 pipelines which support v5 DCP metadata schema.

v0.6.0

27 Feb 21:31
631565e
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Changes:

  • Cromwell-as-a-Service support
    There are new scripts in the repo which help set up the required user accounts for lira to talk to Cromwell-as-a-Service:

  • Logging
    Lira now can send logs to the HCA DCP's centralized logging system. There are also some bug fixes to Lira's logging mechanism.

v0.5.0

08 Feb 21:47
da3801c
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Changes:

  • Python 3 support
    Lira now works in Python 3 as well as Python 2. Previously it worked in Python 2 only.
  • WDL caching
    Lira now caches WDLs instead of downloading them anew for every workflow launch. Caching only works in Python 3. In Python 2 it still downloads the WDLs prior to each workflow launch. Caching is enabled by default but can be turned off by adding "cache_wdls": false to Lira's config.
  • Dry run mode
    For testing purposes, Lira can now run in "dry run" mode, by adding dry_run: true to Lira's config. In this mode, Lira prepares submissions to Cromwell upon receiving notifications but does not actually send the workflows to Cromwell.
  • Config field renamed
    wdl_default_inputs_link has been renamed wdl_static_inputs_link. Existing configurations must be modified to use the new field name or will cause an error on startup.