• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

Clinical-Genomics / trailblazer
88%

Build:
DEFAULT BRANCH: master
Repo Added 14 Mar 2018 08:15AM UTC
Files 114
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

LAST BUILD ON BRANCH master
branch: master
CHANGE BRANCH
x
Reset
  • master
  • 2.1.2
  • 2.2.0
  • 2.2.0b
  • 2.2.1-beta
  • 3.0.0
  • 3.1.0
  • 3.1.1
  • 3.1.2
  • 3.1.4
  • 3.1.5
  • 3.1.6
  • 3.1.7
  • 3.2.0
  • 3.2.1
  • 3.2.2
  • 3.2.3
  • 3.2.4
  • 315-fix-analysis-status
  • 342-fix-search-bug
  • 4.0.0
  • 4.0.1
  • 4.1.0
  • 4.2.0
  • 4.3.0
  • 4.3.1
  • 4.3.2
  • 4.3.3
  • 5.0.0
  • 6.0.0
  • 6.0.3
  • 6.1.0
  • 6.1.1
  • 6.3.0
  • 6.3.1
  • 6.4.0
  • 6.4.1
  • 6.4.2
  • 6.4.3
  • 6.4.4
  • 6.4.5
  • 6.5.0
  • 6.6.0
  • 6.7.0
  • 6.7.1
  • 6.7.2
  • 6.8.0
  • 6.8.1
  • 6.8.2
  • 6.8.3
  • 6.8.4
  • 74-support-filtering-on-delivered
  • CGH_files
  • CI/add-jobs
  • MIP7.1-dev
  • Readd-nuxt-app
  • Remove-nuxt-application
  • Revert-nuxt
  • Solve-issue-nuxt
  • abstract-away-slurm-cli
  • accept-email
  • accept-on-behalf-header
  • accept-workflow-id
  • add-analysis-in-cancel
  • add-cancellable-bool-to-response
  • add-delivery-table
  • add-endpoint-error-handling
  • add-filter-on-status
  • add-git-lint
  • add-integration-tests
  • add-is-hidden-parameter
  • add-keycloak
  • add-missing-indices
  • add-missing-init-file
  • add-oauth-client
  • add-order-analysis-creation
  • add-order-to-analyses
  • add-patch-endpoint
  • add-slurm-api
  • add-slurm-api-service
  • add-slurm-cli-service
  • add-slurm-client
  • add-slurm-services
  • add-summary-endpoint
  • add-ticket-number-to-analysis
  • add-to-comment
  • add-token-verification
  • add-total-count
  • add-tower-id-to-analysis
  • add-tower-missing-file-handling
  • add-typed-mock
  • add-upload-jobs
  • add-user-abbreviations
  • add-user-signatures
  • add-user-verification
  • add-visible-query-param
  • add/express-qos
  • add_alembic
  • add_config_model
  • add_docker
  • add_fail_to_temp_status
  • add_flag
  • add_io_json
  • add_isort
  • add_pre_commit
  • add_qos_maintenance
  • add_ruff
  • add_wts_as_data_analysis
  • adjust-redirect
  • attempt-certs
  • befriend-balsamic
  • beta
  • cancel-analysis
  • cancel-tower-analysis-with-stored-workflow-id
  • cancel_tower
  • cancel_tower_workflow
  • case_id_again
  • centralize-tower-setup
  • cgvs-move
  • click-freeze
  • commit-before-response
  • continues-when-mip-data-is-missing
  • dependabot/npm_and_yarn/nuxt/elliptic-6.5.3
  • dependabot/npm_and_yarn/nuxt/eslint-4.18.2
  • dependabot/npm_and_yarn/nuxt/jquery-3.4.0
  • dependabot/npm_and_yarn/nuxt/jquery-3.5.0
  • dependabot/npm_and_yarn/nuxt/jquery-3.5.1
  • dependabot/npm_and_yarn/nuxt/lodash-4.17.15
  • dependabot/npm_and_yarn/nuxt/lodash-4.17.19
  • dependabot/npm_and_yarn/nuxt/lodash.template-4.5.0
  • dependabot/npm_and_yarn/nuxt/node-fetch-2.6.1
  • dependabot/pip/jinja2-3.1.5
  • dependabot/pip/werkzeug-3.0.6
  • deployment-sop
  • depr_test
  • develop
  • dockerize-cli
  • ensure-upload-jobs-are-not-overwritten
  • extract-slurm-client-error-handling
  • feat/api-queries
  • feat/better-job-names
  • feat/cancel-by-name
  • feat/deploy_to_pypi
  • feat/detach-tb-3
  • feat/dockerize
  • feat/failtext-in-column
  • feat/get-analyses-by-comment
  • feat/integrate-balsamic-tb
  • feat/query-by-comment
  • feat/remove-comment
  • feat/remove-confighandler
  • feat_add_mipflag
  • filter-out-non-uploaded
  • filter-rsync-analyses
  • filter-type-of-analyses
  • fix-add-pendibg
  • fix-alembic-migration
  • fix-balsamic-filter
  • fix-balsamic-filtering
  • fix-batch-handling
  • fix-broken-dependencies
  • fix-cancel
  • fix-cancel-response
  • fix-cancelled-bug
  • fix-circular-import
  • fix-cli-images
  • fix-comment
  • fix-delete-comment
  • fix-delivered
  • fix-enum-spelling
  • fix-image-vulnerabilities
  • fix-install-workflow
  • fix-job-id-parsing
  • fix-job-serialization
  • fix-jobs-missing-in-response
  • fix-latest-analysis
  • fix-logging
  • fix-marshmallow-validation
  • fix-microsalt
  • fix-microsalt-bug
  • fix-missing-cancellable-field
  • fix-missing-ticket
  • fix-missing-type
  • fix-naming
  • fix-pydantic-warning
  • fix-pypi
  • fix-refresh-token
  • fix-ruff
  • fix-scaling
  • fix-scan-action
  • fix-slurm-api-interaction
  • fix-slurm-client
  • fix-slurm-job-info
  • fix-slurm-model
  • fix-smells
  • fix-tower-bug
  • fix-tower-response-after-update
  • fix-tower-status-bug
  • fix-types
  • fix-unknown-interpretation
  • fix-upload-job-update
  • fix/cg-clean-mipauto-mip-backwards-compat
  • fix/decouple-trailblazer-google
  • fix/force-delete
  • fix/googleuser-change
  • fix/namespace
  • fix/parse_configs_ambiguously
  • fix/remove-em-as-codeowner
  • fix/remove-pytest-from-prod-deps
  • fix/set-analysis-completed-comment
  • fix_analysis_failed_jobs
  • fix_analysis_failed_jobs_api
  • fix_delete_analysis
  • fix_long_timestamps
  • fix_looponfailroots
  • fix_server
  • fix_status_null
  • fix_time_elapsed
  • fix_time_tower
  • fix_tower_timestamp_conversion
  • fix_wrong_tb_status
  • fix_yaml
  • fix_zerodivision
  • fixes-more-obsolete-dependencies
  • fixes-obsolete-dependencies
  • force-cleaning-and-deletion
  • get_analysis
  • github_actions
  • github_actions_2
  • github_actions_3
  • gustav_test_branch
  • handle-failed-login
  • improve-env-name
  • improve-logging-for-failing-scan
  • improve-patch
  • include-case-ids-in-summary
  • include-hidden-when-searching
  • include-order-id-in-analysis-response
  • include-upload-jobs-in-analysis-response
  • make-abbreviation-non-nullable
  • make-delivered-fields-nullable
  • make_config_path_optional
  • migtate_add_user_to_createhandler
  • mip-dna-v8.0
  • mip-dna-v8.2
  • mip-pedigree
  • mip-rd-rna
  • mip6
  • mip7-command
  • mip_family_id_compatibility
  • mip_files
  • mip_parse_sampleinfo
  • missing-qccollect
  • modify_travis
  • move-rsync-filtering
  • move_start_of_mip_to_cg
  • mvp-balsamic
  • parse_qcmetrics
  • patch-analysis-endpoint
  • patch-pending-tower-analyses
  • patch-scan
  • patch-search
  • patch-status-calc
  • patch-status-update
  • patch-test
  • patch-update
  • patch-update-visibility
  • patch-upload-jobs
  • pin-docker-base-image-version
  • progress_as_fraction
  • quick_fix_tw_status
  • rank_model_version_from_get_trending
  • reduce-action-duplication
  • refaactor-get-analyses-in-ls-cmd
  • refactor-analyses
  • refactor-analyses-filtering
  • refactor-api-layer
  • refactor-data_analysis-and-pipeline-to-workflow
  • refactor-endpoints
  • refactor-fastq-workflow
  • refactor-linters
  • refactor-sql-filter-function-names
  • refactor-to-PEP-0663
  • refactor-to-PEP-604
  • refactor-to-pep-0585
  • refactor-tower-client
  • refactor_add_comment
  • refactor_add_pending_analysis
  • refactor_add_user
  • refactor_basehandler
  • refactor_cancel_analysis
  • refactor_cancel_slurm_job
  • refactor_constants
  • refactor_date_module
  • refactor_delete_analysis
  • refactor_get_analysis
  • refactor_get_latest_analysis
  • refactor_job
  • refactor_job_in_update_slurm_jobs
  • refactor_mark_analyses_deleted
  • refactor_query_slurm
  • refactor_query_tower
  • refactor_query_tower_2
  • refactor_reading_squeue_output
  • refactor_set_analysis_status
  • refactor_set_analysis_uploaded
  • refactor_sql_aggregate_failed
  • refactor_sql_analysis
  • refactor_sql_archive_user
  • refactor_sql_info
  • refactor_sql_user
  • refactor_sql_users
  • refactor_update_analysis_from_slurm_output
  • refactor_update_jobs
  • refactor_update_ongoing_analyses
  • refactor_update_run_status
  • refactor_update_tower_run_status
  • refresh-token
  • remove-action
  • remove-alchy
  • remove-avatar
  • remove-balsamic-qc
  • remove-is_deleted
  • remove-pylint-config
  • remove-unused-code
  • remove-unused-endpoints
  • remove-unused-job-param
  • remove-unused-query-analyses
  • remove-unused-reformat-logic
  • remove-user-from-response
  • remove_empty_fixture_call
  • remove_get_latest_analysis_status
  • remove_is_latest_analysis_completed
  • remove_is_latest_analysis_failed
  • remove_is_latest_analysis_ongoing
  • remove_python-dateutil
  • remove_test_fixture_prefix
  • removes-mip
  • rename-family-to-case
  • rename-sars-cov-2-to-mutant
  • report-delivered-correctly
  • return-delivery-data
  • return-most-recent-failed-job
  • reverse-8-1-1
  • revert
  • revert-132-reverse-8-1-1
  • revert-507-add-token-verification
  • revert-510-add-token-verification
  • revert-68-mip-rd-rna
  • revert-latest-failed
  • revert-old
  • revert-refactoring
  • rework-delivered-counting
  • rewriting_trending_from_mip6_into_mip5
  • rm-conda-env-and-use-container
  • rm_docutils
  • rm_get_elapsed_time
  • rm_mip_start
  • rm_models_import
  • rm_pytest_yield
  • rm_sql_jobs_function
  • rm_trailblazer_check
  • rm_travis
  • rm_universal_config_option
  • rna-analysis-in-hk
  • rnafusion_support
  • scan-containers
  • set-analysis-to-fail
  • set-upload-date-fastq
  • set_status_cli
  • show-failed-last-month
  • speed-up-analyses-endpoint
  • speedup-retrieval-of-analyses
  • speedup-retrieving-latest-failed-job
  • store-multiqc
  • str-vcf
  • support-slurm-cli-or-api
  • tag-image-with-version
  • test-before-request
  • test-fix
  • test-rest-api
  • test_scope
  • test_server
  • test_server_2
  • test_server_3
  • test_server_4
  • testing-tb-on-k
  • travis-3.7
  • tw_commplete_as_qc
  • udate-werkzug
  • unfreeze_pytest
  • uodate-python
  • update-PR-template
  • update-black
  • update-black-and-ruff
  • update-bootstrap
  • update-certs
  • update-cli-image
  • update-code-owners
  • update-dependencies
  • update-deploy-instructions
  • update-jinja-2
  • update-jinja2
  • update-jquery
  • update-linters
  • update-order-status
  • update-readme
  • update-slurm-upload-jobs
  • update-upload-jobs
  • update-vue-app-packages
  • update_actions
  • update_black
  • update_code_owners
  • update_codeowners
  • update_deps
  • update_docker_actions
  • update_name_for_mip6flag
  • update_name_for_mip6flag_again
  • update_pydantic
  • update_python
  • update_pythonn
  • update_readme
  • update_ruff
  • updates-bootstrap
  • upgrade-deploy-instructions
  • upgrade-python
  • upgrade-sqlalchemy
  • upgrades-bootstrap-to-4.3.x
  • uploaded-at-column
  • usalt
  • use-abbrev
  • use-id-token
  • use-latest-analysis
  • use-poetry
  • use-sacct
  • user-endpoints

20 May 2026 02:03PM UTC coverage: 88.012% (-0.2%) from 88.221%
26167702135

push

github

web-flow
Improve patch analysis test (#535) (patch)

### Fixed

- More granular assertions in the patch_analysis test

2107 of 2394 relevant lines covered (88.01%)

0.88 hits per line

Relevant lines Covered
Build:
Build:
2394 RELEVANT LINES 2107 COVERED LINES
0.88 HITS PER LINE
Source Files on master
  • Tree
  • List 114
  • Changed 1
  • Source Changed 0
  • Coverage Changed 1
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
26167702135 master Improve patch analysis test (#535) (patch) ### Fixed - More granular assertions in the patch_analysis test push 20 May 2026 02:04PM UTC web-flow github
88.01
26023389793 master Test before_request (#529) (patch) Tests for authentication in trailblazer that is performed in the before_request method --------- Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: islean <isak.ohl... push 18 May 2026 08:53AM UTC web-flow github
88.22
25432460426 master Add typed mock module (#532) (patch) ### Added - Typed mock module push 06 May 2026 11:28AM UTC web-flow github
87.8
23847949400 master accept on-behalf-of header (#527)(patch) ## Description Add support for authentication on behalf of a valid user To be merged at the same time as https://github.com/Clinical-Genomics/cg/pull/4976 ### Added - Support for authentication on behal... push 01 Apr 2026 12:13PM UTC web-flow github
87.8
23787795332 master Fix trailblazer to commit all or none (#528) (patch) ## Description The update handler commits every time an entry is modified. For the functions regarding updating analyses, we moved the commit calls to the service layer, so that we could do a f... push 31 Mar 2026 08:26AM UTC web-flow github
87.91
23184085171 master Change tower mapping of status: unknown, to Error instead of failed (#526) (patch) ### Changed - Seqera platform status unknown is now translated tb status Error instead of Failed ---- Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@user... push 17 Mar 2026 07:56AM UTC web-flow github
87.75
23008243668 master update type of exit attribute in TowerTask from str to int (#525) ## Description The Tower response for endpoint `/workflow/{workflowId}/tasks` gives an attribute `exit` as an int, but the model that parses the response expects a str. This PR cha... push 12 Mar 2026 02:56PM UTC web-flow github
87.75
20337151192 master Accept empty string as config_path for slurm analyses (#524) ## Description Raw data analyses will add an analysis with `config_path` as an empty string and `slurm` as workflow manager. Changes made to the validation [here](https://github.com/Cl... push 18 Dec 2025 12:36PM UTC web-flow github
0.0
20237019422 master Make analysis config_path optional (#523) ## Description The `config_path` of an Analysis is only used when the workflow manager is Slurm and no such file is longer being created for most Nextflow pipelines, therefore it should not be required f... push 15 Dec 2025 03:08PM UTC web-flow github
87.75
19302692594 master Add indices to job table (#520) (patch) ### Added - Index on job.job_type - Index on job.status push 12 Nov 2025 03:29PM UTC web-flow github
87.71
See All Builds (2423)
  • Repo on GitHub
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2026 Coveralls, Inc