Skip to content

Latest commit

 

History

History
461 lines (427 loc) · 42.9 KB

CHANGELOG.md

File metadata and controls

461 lines (427 loc) · 42.9 KB
Raw

Release 0.20.3

  • [WM-2560] Update WDL version of GDCWholeGenomeSomaticSingleSample to 1.3.1 (#632)

Release 0.20.2

  • [GH-1695] Fix the "increment BAM version in Clio" again. (#626)

Release 0.20.1

  • [GH-1691] Fix the SG/GDC increment the add_bam version in Clio hack. (#623)

Release 0.20.0

  • [GH-1681] SG/GDC is reprocessing CRAMs and running into Clio update conflicts. (#620)
  • [GH-1674] wfl.module.aou/add-aou-workload! should not add to a stopped workload. (#617)

Release 0.19.1

  • [GH-1686] Deploy WFL to point at ExternalExomeReprocessing_v3.1.7 and pick up picard-cloud:2.26.10. (#618)
  • [GH-1667] Don't delete a Firecloud entity before a Rawls batchUpsert. (#616)

Release 0.19.0

  • [GH-1678] When monitoring source load tags, match prefix instead of exact match. (#614)
  • [GH-1652] Finish fixing TDR problems. (#605)

Release 0.18.5

  • [GH-1671] create-submission! swaps arguments to submit-method. (#612)

Release 0.18.4

  • [GH-1666] Pick up GDCWholeGenomeSomaticSingleSample_v1.3.0 in sg module. (#610)
  • [GH-1654] Admit memory retry multiplier. (#608)

Release 0.18.3

  • [GH-1658] Shouldn't wfl.service.rawls/batch-upsert handle Boolean attributes? (#607)
  • [GH-1653] TDR snapshot direct links have changed (#606)

Release 0.18.2

  • [GH-1652] Fix PrimaryKey mumble cannot be a column with fileref type errors from TDR. (#603)
  • [GH-1651] Re-deploy WFL to pick up new version of WGS to support setting memory_multiplier in SortSam. (#603)

Release 0.18.1

  • [GH-1645] Update wfl.module.wgs/workflow-wdl to allow overriding read_length in CollectRawWgsMetrics. (#600)
  • [GH-1644] Drop delete-directory and copy-directory from wfl.util. (#600)

Release 0.18.0

  • [GH-1623] workloads/update-workload! should define own transactions (#597)
  • [GH-1640] Broken Terra Submission links in completed workflow Slack messages (#598)
  • [GH-1639] Pin jinja2 version for mkdocks compatibility (#596)
  • [GH-1433] No TDR temporary snapshots in tests (#595)
  • [GH-1619] Add workload info to sink logs (#594)
  • [GH-1638] Disable link unfurling when Slacking watchers (#593)

Release 0.17.0

  • [GH-1592] [GH-1635] Notify Slack watchers on Terra submission creation (#591)
  • [GH-1593] Notify Slack watchers on failed TDR snapshot jobs (#590)
  • [GH-1618] Add workload info to executor logs (#589)
  • [GH-1633] Remove WFL_SLACK_ENABLED feature switch (#587)

Release 0.16.0

  • [GH-1629] TerraExecutor gets method configuration version from Firecloud (#585)
  • [GH-1553] [GH-1604] Add error handling to Slack service (#584)
  • [GH-1628] Look at the first 7 workloads returned in test-workflows-by-filters. (#583)
  • [GH-1617] Consistent workload representation for logs (#579)
  • [GH-1624] Rename covid -> staged in code, docs (#580)

Release 0.15.2

  • [GH-1622] Fix logging and logging_level API. (#581)
  • Update CHANGELOG and version from main.

Release 0.15.1

  • [GH-1620] Set the API's image pullPolicy to Always. (#576)

Release 0.15.0

  • [GH-1609] Make do-or-nil log at :debug level. (#574)
  • [GH-1566] Add workload info to logs (#552)
  • [GH-1608] Pull WFL v0.14.x version, changelog into develop (#573)

Release 0.14.1

  • [GH-1604] Disable / hide Slacking behind WFL_SLACK_ENABLED (#571)

Release 0.14.0

  • [GH-1607] wfl.log/stdout-logger should handle JSON-incompatible edn (#569)
  • [DDO-1920] Configure GKE LB Backend Service timeout in Helm (#564)
  • [GH-1598] Update TerraExecutor documentation (#566)

Release 0.13.0

  • [GH-1539] Stop started workloads in system tests (#562)
  • [GH-1563] [GH-1573] TerraDataRepoSource polls row metadata table (#559)
  • [GH-1433] Test TDR snapshot creation within temporary dataset (#561)
  • [GH-1578] TerraDataRepoSource filters old rows before reducing (#560)
  • [GH-1542] TerraExecutor notifies Slack watchers on workflow completion (#553)

Release 0.12.1

  • [GH-1586] Run AoU pipeline with the Arrays_v2.6.3 WDL. (#557)
  • [GH-1527] Remove Firecloud calls when fetching TerraExecutor workflows (#543)

Release 0.12.0

  • [GH-1581] Run AoU pipeline with the Arrays_v2.6.2 WDL. (#554)
  • [GH-1540] Apply User Comments to Terra Submissions (#551)
  • [GH-1560] TerraExecutor tries to set root entity table on submission (#550)
  • [GH-1555] add null check to rename-gather-bulk (#549)

Release 0.11.0

  • [GH-1526] Release "Arrays_v2.6.0" (#547)
  • [GH-1546] Increment minor version to 0.11.0 (#545)
  • [GH-1506] Add some documentation for changing the logging level (#546)
  • [GH-1465] Specify TDR Polling Interval (#542)
  • [GH-1521] Pull v0.10.0 changelog into develop (#544)
  • [GH-1525] Document TerraWorkspaceSink identifier changes (#535)
  • [GH-1516] Documentation updates - TerraExecutor retry (#539)

Release 0.10.0

  • [GH-1475] Update test inputs buckets (#538)
  • [GH-1529] Bump WFL develop version to 0.10.0 (#537)
  • [GH-1474] [GH-1475] [GH-1494] TDR Sink Changes (#520)
  • [GH-1522] TerraWorkspaceSink: identifier can be a workflow input (#534)
  • [GH-1515] WFL-created TDR snapshots include table in name (#536)
  • [GH-1463] WFL API retry by status also requires submission id (#525)
  • [GH-1473] Update GitHub Pages with new Swagger access (#516)
  • [GH-1448] Exceptions fail to be logged as JSON. (#531)
  • [GH-1472] Merge main into develop (#533)
  • [GH-1517] Add automated test for updating method configurations with mismatched versions (#528)
  • [GH-1517] Log instead of throw on TerraExecutor method config version mismatch (#527)

Release 0.9.24

  • Fix WFL deployment. (#526)

Release 0.9.0

  • Fix merge conflicts around logging in server.clj.
  • Trial merge of main to develop.
  • GH-1476 Log failed snapshot creation job's metadata and result (#518)
  • GH-1373 rename removeSucceeded in retry runbook (#519)
  • Updating the version for the develop branch to 0.9.0 (#517)
  • GH-1444 TerraDataRepoSource should not snapshot more frequently than every 20 min (#513)
  • Bump AoU Arrays.wdl version to 2.4.1 to drop default (#514)
  • GH-1462: Make :watchers key always optional. (#515)
  • Keep non-null inputs and options from "Failed" workflows. (#508)
  • GH-1446: fix system tests again (#502)
  • GH-1450 Add retry attribute to TerraDataRepoSource type and instances (#505)
  • GH-1454 Update covid and executor integration tests to reflect updated method configuration version (#504)
  • GH-1439 Succeeded workflow status should be permissible to retry (#503)
  • [GH-1441] Stop swallowing UserExceptions (#501)
  • [GH-1353] Fix spec error when skipValidation sent (#497)
  • Remove the UI component of WFL. (#499)
  • Add a badge for WFL nightly test. (#500)
  • Add a nightly system test against dev WFL (#498)
  • [GH-1301] Add Slack watcher support for user exceptions. (#467)
  • Github actions should build docs on develop. (#495)
  • [GH-1418] sourceLocation null fix (#487)
  • [GH-1303] Google Cloud Logging Alerts (#486)

Release 0.8.2

  • [GH-1454] Update covid and executor integration tests to reflect updated method configuration version (#504)
  • [GH-1394] Update post-retry error maps per QA feedback (#494)
  • [GH-1328] Migrate to new Rawls Snapshot V2 endpoints (#493)
  • Mkdocs updates that improve the doc nav and security holes. (#492)
  • Bump path-parse from 1.0.6 to 1.0.7 in /ui (#491)
  • [GH-1430] Remove stage/validate-or-throw and inline their implementations into create-X. (#490)
  • [GH-1395] GitHub Pages updates: COVID, staged workflows, retry functionality (#489)
  • [GH-1416] Document DataRepo Sink (#485)
  • [GH-1425] Expose TerraDataRepoSink Via the HTTP API (#484)
  • [GH-1395] Document the new WFL retry capability for users. (#483)
  • [GH-1419] Terra Executor queue length should consider workflows with null status (#481)
  • [GH-1139] Logging level and configuration (#480)
  • Remove error txt file (#479)
  • [GH-1415] Implement update-sink for TerraDataRepoSink (#478)
  • [GH-1414] Executor falls back to fetching existing snapshot reference (#477)
  • [GH-1314] Start Implementing DataRepo Sink (#476)
  • Logging added to source namespace (#475)
  • [GH-1402] Write Workflow Outputs to the Terra Data Repository (#474)
  • [GH-1405] Add Schema for TerraDataRepoSink (#473)
  • [GH-1411] Describe Workflow Outputs (#471)
  • [GH-1139] Added new log namespace (#470)
  • Remove trim-slashes and fix endpoints in wfl.tools namespace (#469)
  • [GH-1397] Sweep and snapshot dataset row IDs that were missed when polling a dataset (#468)
  • [GH-1409] Add Status Query String to workflows GET request (#466)
  • Fix some namespace issues (#464)
  • GH-1326 Move Sink code to new Namespace (#463)
  • [GH-1398] Fix test-start-aou-workload from polling forever (#462)
  • [GH-1401] Add retry Attribute to TerraExecutorDetails Type and Instances Thereof (#461)
  • Split specs into their specific modules (#460)
  • Changing order of executor block in docs (#459)
  • fix build failures in develop (#458)
  • Phoned a friend @tbl3rd to fix return type hint in executor docs (#457)
  • Clean up my testing code... (#456)
  • Move source and sink Interfaces and Implementations into new namespace (#454)
  • [GH-1294] Migrate to use datasets in prod TDR (#453)
  • [GH-1393]: Add /retry Endpoint (#452)
  • [GH-1346] Document workload Executor and Terra implementation (#451)
  • [GH-1345] Document the workload Source and Implementations (#450)
  • [GH-1347] Document the workload Sink and Terra Workspace sink implementation (#449)
  • Resolving NPM security vulnerabilities (#448)
  • Removing the arrays module and the corresponding integration test (#446)
  • update changelog for v0.7.1 (#445)
    • [GH-1376] Moved generic pipeline processing interfaces from covid -> stage ns (#444)
  • [GH-1375] Fix AoU nightly test: GET /api/v1/workload fails with spec error from invalid creator (#442)
  • update changelog for v0.7.0 (#441)
  • [GH-1371] Lint more. (#439)
  • [GH-1332] wfl.tools.workloads/when-done should not exit prematurely (#438)
  • [GH-1363] Fix Sporadic Firecloud Test Failures (#437)
  • Move docstring and document when true. (#436)
  • Fix broken requirement install command in docs readme (#434)
  • Bump ws from 6.2.1 to 6.2.2 in /ui (#433)
  • [GH-1359] Overwrite Workspace Entity On Sink (#432)
  • [GH-1357] Fix failure to sink workflow outputs (#431)
  • Documenting a Workload (#430)
  • [GH-1356] Fix Coercion Failure for TDR Snapshots Source (#429)
  • [GH-1354] Enforce snapshotReaders are email addresses (#428)
  • [GH-1350] fix Terra Workspace sink validation (#427)
  • [GH-1348] Remove :pipeline from COVID workload request (#426)
  • Add test-covid-workload to parallel test group (#424)
  • [GH-1324] Get or import snapshot (#422)
  • [GH-1331] document /stop and /workflows (#417)
  • bump version in develop to 0.8.0 (#413)
  • [GH-1336] Fix continual snapshot creation (#419)
  • [GH-1333] Fix NullPointerException in TDR Source (#418)
  • [GH-1327] update system tests after /stop changes (#412)
  • [GH-1327] Fix Start After Stop (#411)
  • [GH-1298] TerraWorkspaceSink - verify target entity columns exist (#410)
  • [GH-1323] to-edn (#409)
  • Remove liquibase-core from build dependencies. (#407)
  • [GH-1316] Create submission within TerraExecutor update (#406)
  • [GH-1320] add snapshotReaders to tdr source (#405)
  • Adding flags for skipping validation of source, executor and sink in requests (#404)
  • [GH-1322] TDR Snapshots Source (#403)
  • [GH-1307] GH-1312 Update method configuration using snapshot reference (#402)
  • [GH-1318] Stop Workload Source (#400)
  • [GH-1317] start the workload source (#399)
  • [GH-1314] expose workflows via GET /api/v1/workload/{uuid}/workflows (#397)
  • [GH-1306] Add workflows multimethod for workloads (#396)
    • GH-1216: [TDR New Work Detection] Extend System Tests for COVID processing (#395)
  • [GH-1313] TerraWorkspaceSink/update-sink! (#394)
  • [GH-1417] Remove the "skipped" nil UUID Cromwell status hack. (#393)
  • Bump hosted-git-info from 2.8.8 to 2.8.9 in /ui (#392
  • Bump lodash from 4.17.19 to 4.17.21 in /ui (#390)
  • [GH-1311]: Create/Load COVID workloads (#389)
  • Bump url-parse from 1.4.7 to 1.5.1 in /ui (#388)
  • Update db schema again based on lasted discussions. (#387)
  • [GH-1301] Notify Workload Watchers when "User Visible" Exceptions Occur (#386)
  • [GH-1295] Use Rawls to Import Workflow Outputs (#384)
  • Add multimethods for source, executor and sink operations (#383)
  • Bump ssri from 6.0.1 to 6.0.2 in /ui (#382)
  • [GH-1213] Update DB schema for COVID workload creation (#381)
  • add interactive script ahead of covid-19 demo (#380)
  • [GH-1213] Create covid workload verifications (#379)
  • [GH-1293] fix test-create-submissions-for-entity-set (#378)
  • Update documentation and infrastructure for release candidates (#377)
  • [GH-1215] Import snapshots within COVID workload (#376)
  • [GH-1215] Add snapshot_reference_id to Sarscov2IlluminaFull table schema (#375)
  • Rename rawls/create-snapshot -> create-snapshot-reference (#373)
  • GH-1285: [COVID] Launch submissions through Rawls, and keep track of them (#372)
  • [GH-1222] Check for new work in TDR (#371)
  • Add wfl.service/rawls.clj for interacting directly with Rawls API (#370)
  • Create an interface all COVID work can build on top of. (#369)
  • [GH-1272] Lists are not imported correctly into a Terra Workspace Entity (#368)
  • util/do-or-nil-silently should move to build.clj (#367)
  • Merge v0.6.1 into develop (#366)
  • Release v0.6.1 Patch (#365)
  • [GH-1277] Prevent update loop from terminating (#364)
  • [GH-1284] Fix docker image generation (#363)
  • Update CHANGELOG.md in develop (#362)
  • [GH-1282] Document WFL's support for Somatic Genomes. (#361)
  • bump develop to 0.7.0 (#360)
  • v0.6.0 Release (#359)
  • [GH-1278] Fix SG update-workload! implementation from updating Clio multiple times (#358)
  • GitHub develop infrastructure + release changes (#356)
  • [GH-1226] Support entity set creation when creating submissions. (#353)
  • Bump y18n from 4.0.0 to 4.0.1 in /ui (#352)
  • [GH-1188] Bump GDCWholeGenomeSomaticSingleSample Version When Lantern Release (#351)

Release 0.7.1

  • GH-1375: Fix AoU nightly test: GET /api/v1/workload fails with spec error from invalid creator (#442)

Release 0.7.0

  • Bump ws from 6.2.1 to 6.2.2 in /ui (#433)
  • [GH-1363] Fix Sporadic Firecloud Test Failures (#437)
  • [GH-1361] Disable Failing Tests for v0.7.0 Release (#435)
  • Move docstring and document when true. (#436)
  • Fix broken requirement install command in docs readme (#434)
  • [GH-1359] Overwrite Workspace Entity On Sink (#432)
  • [GH-1357] Fix failure to sink workflow outputs (#431)
  • [GH-1356] Fix Coercion Failure for TDR Snapshots Source (#429)
  • [GH-1354] Enforce snapshotReaders are email addresses (#428)
  • [GH-1325] Get or import snapshot (#422)
  • Bump dns-packet from 1.3.1 to 1.3.4 in /ui
  • [GH-1350] fix Terra Workspace sink validation (#427)
  • [GH-1348] Remove :pipeline from COVID workload request (#426)
  • [GH-1344] Enforce valid email addresses in workload watchers
  • [GH-1341] Fix accepting malformed labels in workload request RR: https://broadinstitute.atlassian.net/browse/GH-1341 Enforce labels are of the form "name:value" where - name starts with a letter followed by any combination of letters, numbers, underscores and dashes - value is any non-blank string not containing :
  • Add test-covid-workload to parallel test group (#424)
  • [GH-1331] document /stop and /workflows (#417)
  • [GH-1339] Prevent Snapshot Job IDs from being clobbered with nils RR: https://broadinstitute.atlassian.net/browse/GH-1339 When we update the status of snapshot creation jobs, we only get the job metadata when the job is complete.As a consequence, nils are propagated up the call stack and the database record is clobbered with nils, including the snapshot_creation_job_id column.
  • [GH-1338] Fix wfl not discovering new dataset rows RR: https://broadinstitute.atlassian.net/browse/GH-1338 This isn't a complete fix sadly but it at least solves the problem for low ingest rate projects like COVID. For now, only updating last_checked when we successfully found new rows in the dataset.
  • [GH-1337] fix create snapshot job always failing RR: https://broadinstitute.atlassian.net/browse/GH-1337 Caused by destructuring the tdr job response with the wrong key.
  • [GH-1336] Fix continual snapshot creation (#419)
  • [GH-1333] Fix NullPointerException in TDR Source (#418)
  • [GH-1327] update system tests after /stop changes (#412)
  • [GH-1327] Fix Start After Stop (#411)
  • GH-1298: TerraWorkspaceSink - verify target entity columns exist (#410)
  • [GH-1323] to-edn (#409)
  • GH-1316 Create submission within TerraExecutor update (#406)
  • [GH-1213] Create covid workload verifications (#379)
  • Remove liquibase-core from build dependencies. (#407)
  • [GH-1320] add snapshotReaders to tdr source (#405)
  • GH-1216: [TDR New Work Detection] Extend System Tests for COVID processing (#395)
  • [GH-1318] Stop Workload Source (#400)
  • [GH-1322] TDR Snapshots Source (#403)
  • GH-1307 GH-1312 Update method configuration using snapshot reference (#402)
  • TerraExecutor/update-executor should update active, failed workflow statuses (#398)
  • [GH-1317] start the workload source (#399)
  • [GH-1314] expose workflows via GET /api/v1/workload/{uuid}/workflows (#397)
  • [GH-1222] Check for new work in TDR (#371)
  • [GH-1306] Add workflows multimethod for workloads (#396)
  • [GH-1215] COVID TerraExecutor/update-executor!
  • [GH-1313] TerraWorkspaceSink/update-sink! (#394)
  • [GH-1311]: Create/Load COVID workloads (#389)
  • Bump lodash from 4.17.19 to 4.17.21 in /ui (#390)
  • Bump hosted-git-info from 2.8.8 to 2.8.9 in /ui (#392)
  • [GH-1301] Notify Workload Watchers when "User Visible" Exceptions Occur (#386)
  • Bump y18n from 4.0.0 to 4.0.1 in /ui (#352)
  • Update db schema again based on lasted discussions. (#387)
  • Bump url-parse from 1.4.7 to 1.5.1 in /ui (#388)
  • GH-1285: [COVID] Launch submissions through Rawls, and keep track of them (#372)
  • [GH-1295] Use Rawls to Import Workflow Outputs (#384)
  • [GH-1215] Import snapshots within COVID workload (#376)
  • Add multimethods for source, executor and sink operations (#383)
  • [GH-1213] Update DB schema for COVID workload creation (#381)
  • add interactive script ahead of covid-19 demo (#380)
  • Bump ssri from 6.0.1 to 6.0.2 in /ui (#382)
  • Update documentation and infrastructure for release candidates (#377)
  • [GH-1293] fix test-create-submissions-for-entity-set (#378)
  • [GH-1215] Add snapshot_reference_id to Sarscov2IlluminaFull table schema (#375)
  • Rename rawls/create-snapshot -> create-snapshot-reference (#373)
  • Add wfl.service/rawls.clj for interacting directly with Rawls API (#370)
  • GH-1272: Lists are not imported correctly into a Terra Workspace Entity (#368)
  • Create an interface all COVID work can build on top of. (#369)
  • GH-1226 Support entity set creation when creating submissions. (#353)
  • util/do-or-nil-silently should move to build.clj (#367)
  • bump develop to 0.7.0 (#360)
  • Snapshot creation uses datetime rather than date (#355)

Release 0.6.1

  • [GH-1277] Prevent update loop from terminating (#364)
  • [GH-1284] Fix docker image generation (#363)

Release 0.6.0

  • GH-1282: Document WFL's support for Somatic Genomes. (#361)
  • GitHub develop infrastructure + release changes (#356)
  • GH-1188: Bump GDCWholeGenomeSomaticSingleSample Version When Lantern Release (#351)
  • [GH-1278] Fix SG update-workload! implementation from updating Clio multiple times (#358)
  • [GH-1221] import snapshots into a workspace (#347)
  • Bump pyyaml from 5.3.1 to 5.4 in /ops (#350)
  • Fix CLIpy. (#349)
  • Ra gh1254 cli changes (#346)
  • [GH-1214] Create TDR Snapshots (#338)
  • Ra gh1254 cli changes (#345)
  • [GH-1244] Lightweight Testing Dataset(s) (#342)
  • Changing cli.py to reflect deployment from helmfile rather than helm (#344)
  • Bump elliptic from 6.5.3 to 6.5.4 in /ui (#343)
  • [GH-1225] POST /api/v1/stop (#337)
  • [GH-1203]: fix reading from vault at load-time (#336)
  • [GH-1172] Start System Test for sarscov2_illumina_all Automation (#334)
  • GH-1191: Plumb WFL_CLIO_URL for production. (#335)
  • [GH-1196] Try to run production data through Somatic Genomes pipeline. (#327)
  • Add workaround for GH-1212. (#333)
  • [GH-1172] Add inputs.edn for sarscov2_illumina_full (#332)
  • [GH-1172] Bulk Ingest Workflow Outputs (#331)
  • Use firecloud api defined by WFL_FIRECLOUD_URL (#329)
  • [GH-1200] Double submit hot-fix 0.5.2 changes. (#330)
  • [GH-1205] TDR schemas for sarscov2_illumina_full pipeline (#328)
  • GH-1163: Support Somatic Genomes in production. (#324)
  • [GH-1181] Add Dispatch for "Object" Type (#325)
  • [GH-1155] Add a BigQuery module for BQ and Terra interactions (#320)
  • [GH-1181] Ingest Workflow Outputs into TDR (#321)
  • [GH-1197] Fix default inputs and options and update documentation about configurations. (#317)
  • Updating AppVersion to the latest tag (0.5.1) (#323)
  • GH-1178: Improve SG tests. (#318)
  • partition by datarepo_ingest_data in assemble_refbased schema (#322)
  • [GH-1176] assemble_refbased workflow outputs schema (#316)
  • fix [GH-1182] by reordering when the Pub/Sub subscription is (#319)
  • [GH-1130] Miscellaneous WFL configuration and build clean up. Remove envs. (#310)
  • Update the environments commit. For the last time? (#315)
  • [GH-1153] Google Cloud Pub/Sub Support for Cloud Storage Notifications (#312)
  • GH-1091: Track Somatic Genomes output in Clio. (#307)
  • [Snack] Fix some bugs and warnings on the frontend (#311)
  • Add docs for GPArrays module (#309)
  • [GH-1145] [AppSec] Add AppSec Github Trivy Action (#308)
  • [Snack] Version the docs (#301)
  • [GH-1144] Helper script for importing Data Repo data into Terra (#306)
  • Move everything around, add abort.sh docs (#302)
  • [GH-1142] Make aou cleanup script backwards compatible (#303)
  • Bump version file to 0.6.0. (#305)

Release 0.5.2

  • Pin to a commit hash.
  • Bump version string.
  • Use WGS wdl on develop branch.

Release 0.5.1

  • Bump version string
  • Use a hot-fix WDL to bypass OOM errors.

Release 0.5.0

  • [GH-1120] Document the usage of Env Vars and fixed an issue with GPArrays system test. (#287)
  • GH-1104: Factor build code out of WFL. (#297)
  • [GH-1129] Avoid NPE in /exec by properly renaming keys (#300)
  • [GH-1105] Update workloads in background periodically (#298)
  • Add retrying page (#299)
  • Get vault_token_path from aou inputs (#293)
  • [GH-1125] Don't finish unstarted workloads (#296)
  • [GH-1090] Automatic SG submission (#280)
  • [GH-1110] Rename cromwell to executor (#294)
  • [GH-1105] Add update loop plumbing (#290)
  • [GH-668] Don't clone WARP, don't zip deps, use HTTP WDLs (#291)
  • [GH-1115] Update directory docs for wfl batching (#292)
  • Update workflow-options.md (#289)
  • Bump axios from 0.19.2 to 0.21.1 in /ui (#288)
  • [GH-1089] SG module (#285)
  • [GH-1086] Make system tests flexible enough to choose Cromwell deployments (#276)
  • [GH-1111] Update AOU cloud fn to handle paths with or without env prefix (#284)
  • [GH-1106] final_gvcf_base_name and base_file_name should be the same as the sample_name (#277)
  • Grab deployment keys from Vault, not secrets (#283)
  • Handle environments in file paths (#282)
  • [GH-1111] Handle Mercury staging messages for AOU (#279)
  • [GH-1114] Fix WFL's Helm chart releaser action (#281)
  • GH-1095: Batch submit workflows to Cromwell (#272)

Release 0.4.0

  • create release candidate for v0.4.0 (#231)
  • graphic updates (#230)
  • Update docs and make improvements during feature bashing (#227)
  • dont serialise empty workflow options if an empty map is specified (#228)
  • [GH-1048] Fix the DataRepo test. (#223)
  • update docs removing id and items (#226)
  • [GH-1063] Remove Serialisation Internals from Workload Responses (#225)
  • [GH-1023] Support querying workloads by project name (#222)
  • update after @tbl3rd's comment (#224)
  • [GH-1061] don't send back defaults when user specifies reference_fasta_prefix (#221)
  • [GH-1045] Arbitrary WGS Inputs (#218)
  • [GH-1045] update docs for wgs + common block changes (#219)
  • [GH-1037] Parallel system test runner (#215)
  • Set default maxRetries option (#220)
  • [GH-1049] Better handling of cram bam in xx and wgs (#216)
  • Documentation updates (#214)
  • [GH-1050] disable wfl.integration.datarepo-test/delivery (#213)
  • [GH-1014] Workflow Options (Final) (#208)
  • [GH-978] Fixes to cleanup script (#212)
  • [GH-978] Give hOps a way to exclude certain AOU files from cleanup (#211)
  • [GH-978] Reap obsolete analysis versions from AOU input bucket (#210)
  • Add documentation about release process and the automation to generate changelog (#206)
  • [GH-1022] make wgs use CromwellWorkflow table. (#204)
  • disable automatic release action (#205)
  • [GH-1024] Make start workload endpoint take a single UUID (#202)
  • [GH-1022] Repurpose external exome table for batch workloads (#203)
  • [GH-1011] update xx docs after changes to input items (#201)
  • use random db name in tests (#200)
  • [GH-1028] Standardize WFL's exception handling (#193)
  • GH-986: Remove dsde-pipelines as WFL's dependency and fix what breaks. (#195)
  • [GH-1035] Add terra module to WFL (#197)
  • update cloud_function after api tidy-ups (#199)
  • some code tidy-ups. (#196)
  • [GH-1013] Item Nesting V2 (#188)
  • [GH-1034] Fix reference_fasta function (#194)
  • [GH-771] WGS updates (#191)
  • [GH-819] External Exome Reprocessing (#139)