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Release 0.10.0 #39

Merged
merged 67 commits into from
Apr 18, 2024
Merged

Release 0.10.0 #39

merged 67 commits into from
Apr 18, 2024

Commits on Dec 12, 2023

  1. Enable organelles subworkflow

    Ksenia Krasheninnikova committed Dec 12, 2023
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  2. Swtich on organelles on github test

    Ksenia Krasheninnikova committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. Update for nextflow secrets in code

    Ksenia Krasheninnikova committed Dec 13, 2023
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  2. Fix CI

    Ksenia Krasheninnikova committed Dec 13, 2023
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  3. Add patch

    Ksenia Krasheninnikova committed Dec 13, 2023
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  4. Fix CI

    Ksenia Krasheninnikova committed Dec 13, 2023
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  5. Add secrets as an extra step

    Ksenia Krasheninnikova committed Dec 13, 2023
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  6. Fix to the order of steps

    Ksenia Krasheninnikova committed Dec 13, 2023
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  7. Remove faulty declaration in ci.yml

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Dec 13, 2023
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  8. Update usage.md

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Dec 13, 2023
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  9. Update README.md

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Dec 13, 2023
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  10. Update test.config

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Dec 13, 2023
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Commits on Dec 15, 2023

  1. New dev branch

    @muffato
    Ksenia Krasheninnikova authored and muffato committed Dec 15, 2023
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  2. Added the template CHANGELOG entry

    @muffato
    muffato committed Dec 15, 2023
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  3. Merge pull request #33 from sanger-tol/0.9.1dev 

    Post-release merge into dev
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Dec 15, 2023
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Commits on Feb 7, 2024

  1. Update ci.yml 

    Change working server name to ubuntu-latest
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 7, 2024
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  2. Merge branch 'dev' into fixes_before_release

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 7, 2024
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Commits on Feb 19, 2024

  1. Add oatk to organelles subworkflow

    Ksenia Krasheninnikova committed Feb 19, 2024
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  2. Prettier fix

    Ksenia Krasheninnikova committed Feb 19, 2024
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  3. eclint fix

    Ksenia Krasheninnikova committed Feb 19, 2024
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Commits on Feb 21, 2024

  1. Test edits to findMitoReference.py script

    Ksenia Krasheninnikova committed Feb 21, 2024
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  2. Add fam to test data

    Ksenia Krasheninnikova committed Feb 21, 2024
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Commits on Feb 26, 2024

  1. Use secret in the module findmitoreference

    Ksenia Krasheninnikova committed Feb 26, 2024
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  2. Update findmitoreference diff

    Ksenia Krasheninnikova committed Feb 26, 2024
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  3. Update ci.yml 

    Try bigger runner
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 26, 2024
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  4. Further increase resources for CI test

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 26, 2024
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  5. Update ci.yml

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 26, 2024
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  6. Update ci.yml

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Feb 26, 2024
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Commits on Mar 13, 2024

  1. Dont purge haplotigs

    Ksenia Krasheninnikova committed Mar 13, 2024
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Commits on Mar 18, 2024

  1. Run organelles pipeline on raw contigs

    Ksenia Krasheninnikova committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. Switch on organelles for github testing

    Ksenia Krasheninnikova committed Mar 19, 2024
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  2. Switch off polishing

    Ksenia Krasheninnikova committed Mar 19, 2024
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  3. Switch on polishing

    Ksenia Krasheninnikova committed Mar 19, 2024
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  4. Polishing is off in CI

    Ksenia Krasheninnikova committed Mar 19, 2024
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  5. Fix longranger versions and switch polishing on for CI

    Ksenia Krasheninnikova committed Mar 19, 2024
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  6. Prettify ci.yml

    Ksenia Krasheninnikova committed Mar 19, 2024
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  7. Missed quotes

    Ksenia Krasheninnikova committed Mar 19, 2024
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  8. Change logic of longranger github container

    Ksenia Krasheninnikova committed Mar 19, 2024
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  9. Login into github for CI

    Ksenia Krasheninnikova committed Mar 19, 2024
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  10. Move login section

    Ksenia Krasheninnikova committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. Enforce copy mode for mitohifi

    Ksenia Krasheninnikova committed Mar 20, 2024
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  2. Update test_github.config 

    Switch polishing off in CI
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Mar 20, 2024
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Commits on Mar 21, 2024

  1. Merge CI test configuration files

    Ksenia Krasheninnikova committed Mar 21, 2024
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  2. Update longranger version

    Ksenia Krasheninnikova committed Mar 21, 2024
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  3. Move CI container for longranger into github config

    Ksenia Krasheninnikova committed Mar 21, 2024
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Commits on Mar 22, 2024

  1. Move test profile configuration to modules.conf

    Ksenia Krasheninnikova committed Mar 22, 2024
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  2. Fix ec checks

    Ksenia Krasheninnikova committed Mar 22, 2024
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  3. Formatting

    Ksenia Krasheninnikova committed Mar 22, 2024
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  4. Merge pull request #27 from sanger-tol/fixes_before_release 

    Enable organelles subworkflow
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Mar 22, 2024
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Commits on Apr 10, 2024

  1. Fix path to the github test dataset

    Ksenia Krasheninnikova committed Apr 10, 2024
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  2. Fix tar keys

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 10, 2024
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  3. Merge pull request #37 from sanger-tol/fixes_before_release 

    Fix path to the github test dataset
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 10, 2024
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Commits on Apr 15, 2024

  1. Bump new version

    Ksenia Krasheninnikova committed Apr 15, 2024
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  2. Update CHANGELOG.md

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 15, 2024
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  3. Dump software versions out of for ORGANELLES subworkflow

    Ksenia Krasheninnikova committed Apr 15, 2024
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  4. Prettier fix

    Ksenia Krasheninnikova committed Apr 15, 2024
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  5. Update README.md

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 15, 2024
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  6. Updated organelles image

    Ksenia Krasheninnikova committed Apr 15, 2024
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  7. Update output.md

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 15, 2024
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  8. Rename the image file

    Ksenia Krasheninnikova committed Apr 15, 2024
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  9. Make sure oatk output is published

    Ksenia Krasheninnikova committed Apr 15, 2024
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Commits on Apr 16, 2024

  1. Add support for plastid for oatk (optional)

    Ksenia Krasheninnikova committed Apr 16, 2024
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  2. Update CHANGELOG.md 

    Updates based on code review
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 16, 2024
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  3. Update output.md 

    Add description about plastid
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 16, 2024
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  4. Update schema description

    Ksenia Krasheninnikova committed Apr 16, 2024
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  5. Update release date

    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 16, 2024
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  6. Merge pull request #38 from sanger-tol/release-0.9.1 

    Release 0.10.0
    @ksenia-krasheninnikova
    ksenia-krasheninnikova authored Apr 16, 2024
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