Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[automated] Merge Develop into Master #2049

Merged
merged 42 commits into from
Nov 12, 2024
Merged

[automated] Merge Develop into Master #2049

merged 42 commits into from
Nov 12, 2024

Commits on Oct 17, 2024

  1. feat(rnaf): adds rna ffpe pipeline, robot steps and purposes

    @BenTopping
    BenTopping committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    f472079 View commit details
    Browse the repository at this point in the history

Commits on Oct 18, 2024

  1. feat(rnaf): removes lrnaf cherrypick in favour of using lbr cherrypick

    @BenTopping
    BenTopping committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    3a9deb7 View commit details
    Browse the repository at this point in the history

Commits on Oct 23, 2024

  1. Refactor pipeline configuration for Hi-C in bespoke PCR 

    This commit refactors the pipeline configuration for Hi-C in the bespoke PCR workflow. The previous configuration included multiple Hi-C library types that are no longer used. This commit removes those unused library types and updates the relationships between the different steps in the workflow.

Related issue: N/A
    @dasunpubudumal
    dasunpubudumal committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    de60306 View commit details
    Browse the repository at this point in the history

  2. Refactor pipeline configuration for Hi-C in bespoke PCR

    @dasunpubudumal
    dasunpubudumal committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    5cfa76a View commit details
    Browse the repository at this point in the history

  3. Refactor active_pipelines_for method in PipelineList

    @dasunpubudumal
    dasunpubudumal committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    b1ce713 View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2024

  1. Update vite to version 5.4.10

    @depfu
    depfu[bot] authored Oct 24, 2024
    Configuration menu
    Copy the full SHA
    c6d8ff4 View commit details
    Browse the repository at this point in the history

  2. Refactor pipeline configuration to include Hi-C in bespoke PCR

    @dasunpubudumal
    dasunpubudumal committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    85c7d58 View commit details
    Browse the repository at this point in the history

  3. Refactor pipeline configuration to include Hi-C in bespoke PCR

    @dasunpubudumal
    dasunpubudumal committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    458297c View commit details
    Browse the repository at this point in the history

  4. Refactor active_pipelines_for method in PipelineList

    @dasunpubudumal
    dasunpubudumal committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    e675ff3 View commit details
    Browse the repository at this point in the history

  5. Refactor pipeline configuration to include Haplotagging in bespoke PCR

    @dasunpubudumal
    dasunpubudumal committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    28ce2af View commit details
    Browse the repository at this point in the history

Commits on Oct 28, 2024

  1. misc: wip rnaf pipeline

    @BenTopping
    BenTopping committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    fe551b2 View commit details
    Browse the repository at this point in the history

  2. Update rexml to version 3.3.9

    @depfu
    depfu[bot] authored Oct 28, 2024
    Configuration menu
    Copy the full SHA
    26834c7 View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2024

  1. Update eslint-plugin-vue to version 9.30.0

    @depfu
    depfu[bot] authored Oct 29, 2024
    Configuration menu
    Copy the full SHA
    4f9550f View commit details
    Browse the repository at this point in the history

Commits on Oct 30, 2024

  1. Customer-requested bed number change

    @KatyTaylor
    KatyTaylor committed Oct 30, 2024
    Configuration menu
    Copy the full SHA
    adebf9a View commit details
    Browse the repository at this point in the history

Commits on Nov 2, 2024

  1. Update oj to version 3.16.7

    @depfu
    depfu[bot] authored Nov 2, 2024
    Configuration menu
    Copy the full SHA
    8fa9c1d View commit details
    Browse the repository at this point in the history

Commits on Nov 5, 2024

  1. Revert "Revert "Y24-022 UI Submit Pool XP tube to traction""

    @seenanair
    seenanair authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    498b2fb View commit details
    Browse the repository at this point in the history

  2. Merge pull request #2048 from sanger/revert-2046-revert-2008-y24-022-… 

    …ui-submit-pool-xp-tube-to-traction

Revert "Revert "Y24-022 UI Submit Pool XP tube to traction""
    @seenanair
    seenanair authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    d3948a3 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #2037 from sanger/scrna-core-bed-verification-chan… 

    …ge-2

Customer-requested bed number change
    @KatyTaylor
    KatyTaylor authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    5938412 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #2031 from sanger/depfu/update/rexml-3.3.9 

    🚨 [security] [ruby] Update rexml 3.3.6 → 3.3.9 (patch)
    @StephenHulme
    StephenHulme authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    e2bf5b3 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #2045 from sanger/depfu/update/oj-3.16.7 

    [ruby] Update oj 3.16.5 → 3.16.7 (patch)
    @StephenHulme
    StephenHulme authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    7db5324 View commit details
    Browse the repository at this point in the history

  6. Update rails to version 7.1.5

    @depfu
    depfu[bot] authored Nov 5, 2024
    Configuration menu
    Copy the full SHA
    5af4eb7 View commit details
    Browse the repository at this point in the history

Commits on Nov 6, 2024

  1. Add bespoke Hi-C configuration to pipeline and remove redundant entri… 

    …es from bespoke PCR
    @dasunpubudumal
    dasunpubudumal committed Nov 6, 2024
    Configuration menu
    Copy the full SHA
    ae416aa View commit details
    Browse the repository at this point in the history

  2. WIP flagging new pipeline config

    @dasunpubudumal
    dasunpubudumal committed Nov 6, 2024
    Configuration menu
    Copy the full SHA
    9a56469 View commit details
    Browse the repository at this point in the history

  3. WIP flagging hic norm plate purpose

    @dasunpubudumal
    dasunpubudumal committed Nov 6, 2024
    Configuration menu
    Copy the full SHA
    a6bc921 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #2041 from sanger/depfu/update/group/rails-7.1.5 

    🚨 [security] [ruby] Update rails 7.1.4 → 7.1.5 (patch)
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    d3da88f View commit details
    Browse the repository at this point in the history

  5. Merge pull request #2020 from sanger/depfu/update/yarn/vite-5.4.10 

    [js] Update vite 5.4.7 → 5.4.10 (patch)
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    6145703 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #2035 from sanger/depfu/update/yarn/eslint-plugin-… 

    …vue-9.30.0

[js] Update eslint-plugin-vue 9.20.1 → 9.30.0 (minor)
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    a0ea116 View commit details
    Browse the repository at this point in the history

  7. Update Node.js to version 22.11.0

    @depfu
    depfu[bot] authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    2c1f96d View commit details
    Browse the repository at this point in the history

  8. Merge pull request #2004 from sanger/y24-265-rna-ffpe 

    Y24-265 - RNA FFPE pipeline
    @BenTopping
    BenTopping authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    2223eb7 View commit details
    Browse the repository at this point in the history

  9. Merge pull request #2038 from sanger/depfu/engine/yarn/nodejs-22.11.0 

    [js] Update Node.js 20.16.0 → 22.11.0
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    c01e8ce View commit details
    Browse the repository at this point in the history

  10. Update selenium-webdriver to version 4.26.0

    @depfu
    depfu[bot] authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    a09fcce View commit details
    Browse the repository at this point in the history

  11. Merge pull request #2053 from sanger/depfu/update/selenium-webdriver-… 

    …4.26.0

[ruby] Update selenium-webdriver 4.23.0 → 4.26.0 (minor)
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    0ef9d9b View commit details
    Browse the repository at this point in the history

  12. build: remove rspec-rails version lock and update 

    The lock was previously put in place as part of the update to Rails 7
    @StephenHulme
    StephenHulme committed Nov 6, 2024
    Configuration menu
    Copy the full SHA
    30d6457 View commit details
    Browse the repository at this point in the history

  13. Merge pull request #2054 from sanger/sh51/remove-rspec-rails-version-… 

    …lock

build: remove rspec-rails version lock and update
    @StephenHulme
    StephenHulme authored Nov 6, 2024
    Configuration menu
    Copy the full SHA
    4a05005 View commit details
    Browse the repository at this point in the history

Commits on Nov 7, 2024

  1. Update @vitest/coverage-v8 to version 2.1.4

    @StephenHulme
    StephenHulme committed Nov 7, 2024
    Configuration menu
    Copy the full SHA
    64ef6ba View commit details
    Browse the repository at this point in the history

  2. build: update vitest to compatible version

    @StephenHulme
    StephenHulme committed Nov 7, 2024
    Configuration menu
    Copy the full SHA
    b36de72 View commit details
    Browse the repository at this point in the history

  3. build: regenerate lockfile

    @StephenHulme
    StephenHulme committed Nov 7, 2024
    Configuration menu
    Copy the full SHA
    caadb9e View commit details
    Browse the repository at this point in the history

  4. Merge pull request #2023 from sanger/y24-335-barcode-for-norm-plate-t… 

    …ests

Y24 335 barcode for norm plate tests
    @dasunpubudumal
    dasunpubudumal authored Nov 7, 2024
    Configuration menu
    Copy the full SHA
    779563f View commit details
    Browse the repository at this point in the history

Commits on Nov 8, 2024

  1. Merge pull request #2036 from sanger/depfu/update/yarn/@vitest/covera… 

    …ge-v8-2.1.4

[js] Update @vitest/coverage-v8 2.0.5 → 2.1.4 (minor)
    @StephenHulme
    StephenHulme authored Nov 8, 2024
    Configuration menu
    Copy the full SHA
    0402678 View commit details
    Browse the repository at this point in the history

Commits on Nov 12, 2024

  1. misc: unwip rnaf pipeline

    @BenTopping
    BenTopping committed Nov 12, 2024
    Configuration menu
    Copy the full SHA
    38c1eb9 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #2066 from sanger/unwip-rna-ffpe 

    misc: unwip rnaf pipeline
    @BenTopping
    BenTopping authored Nov 12, 2024
    Configuration menu
    Copy the full SHA
    7737ff3 View commit details
    Browse the repository at this point in the history

  3. misc: bumps release version

    @BenTopping
    BenTopping committed Nov 12, 2024
    Configuration menu
    Copy the full SHA
    6f3529a View commit details
    Browse the repository at this point in the history