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Release PR for 2.5.2 #568

Merged
merged 69 commits into from
Feb 2, 2024
Merged

Release PR for 2.5.2 #568

merged 69 commits into from
Feb 2, 2024

Commits on Nov 17, 2023

  1. Post-release version bump to dev

    @jfy133
    jfy133 committed Nov 17, 2023
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  2. Harshil align

    @jfy133
    jfy133 authored Nov 17, 2023
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  3. Merge pull request #542 from nf-core/post-release-version-bump 

    Post-release version bump to dev
    @jfy133
    jfy133 authored Nov 17, 2023
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Commits on Nov 21, 2023

  1. fix: centrifuge db needs to be a tuple

    @maxibor
    maxibor committed Nov 21, 2023
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Commits on Nov 24, 2023

  1. patch commits

    @maxibor
    maxibor committed Nov 24, 2023
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Commits on Dec 5, 2023

  1. fix: remove duplicated code

    @maxibor
    maxibor committed Dec 5, 2023
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  2. cleanup: remove dump logs

    @maxibor
    maxibor committed Dec 5, 2023
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Commits on Dec 19, 2023

  1. Template update for nf-core/tools version 2.11

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    nf-core-bot committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. Template update for nf-core/tools version 2.11.1

    @nf-core-bot
    nf-core-bot committed Dec 20, 2023
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Commits on Jan 15, 2024

  1. First pass of bug fix, to be tested again

    @jfy133
    jfy133 committed Jan 15, 2024
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Commits on Jan 16, 2024

  1. Update BUSCO db in tests to latest version as older version not anymo… 

    …re accessible
    @jfy133
    jfy133 committed Jan 16, 2024
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  2. Update last URL

    @jfy133
    jfy133 committed Jan 16, 2024
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  3. Merge branch 'dev' into nf-core-template-merge-2.11

    @jfy133
    jfy133 authored Jan 16, 2024
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  4. Fix BUSCO download links due to deprecation of old verison of db in t… 

    …ests
    @jfy133
    jfy133 authored Jan 16, 2024
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  5. Simplify CAT_FASTQ branch condition, and remove misplaced flatten()

    @jfy133
    jfy133 committed Jan 16, 2024
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  6. Remove unnecessary space

    @jfy133
    jfy133 authored Jan 16, 2024
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  7. Remove leftover TODO

    @jfy133
    jfy133 authored Jan 16, 2024
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  8. Better commenting

    @jfy133
    jfy133 authored Jan 16, 2024
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  9. Remove superfluous .map()

    @jfy133
    jfy133 committed Jan 16, 2024
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  10. Add comment for of run merging group tuple structure

    @jfy133
    jfy133 committed Jan 16, 2024
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  11. Fix linting

    @jfy133
    jfy133 committed Jan 16, 2024
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  12. Update nextflow.config to fix docker.runOptions

    @CarsonJM
    CarsonJM authored Jan 16, 2024
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Commits on Jan 17, 2024

  1. Merge pull request #553 from nf-core/nf-core-template-merge-2.11 

    Important! Template update for nf-core/tools v2.11
    @jfy133
    jfy133 authored Jan 17, 2024
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Commits on Jan 19, 2024

  1. Merge branch 'dev' into fix-cat-se-data-dev

    @jfy133
    jfy133 committed Jan 19, 2024
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  2. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jan 19, 2024
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Commits on Jan 26, 2024

  1. Update workflows/mag.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @maxibor @jfy133
    maxibor and jfy133 authored Jan 26, 2024
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  2. Update workflows/mag.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @maxibor @jfy133
    maxibor and jfy133 authored Jan 26, 2024
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  3. Update subworkflows/local/gtdbtk.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @maxibor @jfy133
    maxibor and jfy133 authored Jan 26, 2024
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  4. Update subworkflows/local/gtdbtk.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @maxibor @jfy133
    maxibor and jfy133 authored Jan 26, 2024
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  5. Update CLASSIFYWF to fix find glob issue

    @jfy133
    jfy133 committed Jan 26, 2024
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  6. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jan 26, 2024
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  7. feat: add CAT summary to bin_summary table

    @maxibor
    maxibor committed Jan 26, 2024
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  8. Merge branch 'patch_2_5_1' of github.com:maxibor/mag into add_cat_2_s… 

    …ummary
    @maxibor
    maxibor committed Jan 26, 2024
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  9. chore: update changelog

    @maxibor
    maxibor committed Jan 26, 2024
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  10. fix: CAT global summary channel

    @maxibor
    maxibor committed Jan 26, 2024
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  11. readd changes from PR

    @maxibor
    maxibor committed Jan 26, 2024
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  12. fix: cat_summary is the variable name

    @maxibor
    maxibor committed Jan 26, 2024
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  13. Merge pull request #548 from maxibor/patch_2_5_1 

    Patch of #534 into dev for v2.5.1
    @jfy133
    jfy133 authored Jan 26, 2024
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  14. Merge pull request #558 from nf-core/fix-cat-se-data-dev 

    Fix malformed input to MEGAHIT with non-run-merged SEdata
    @jfy133
    jfy133 authored Jan 26, 2024
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Commits on Jan 29, 2024

  1. Template update for nf-core/tools version 2.12

    @nf-core-bot
    nf-core-bot committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. Merge remote-tracking branch 'upstream/dev' into add_cat_2_summary

    @maxibor
    maxibor committed Jan 30, 2024
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Commits on Feb 1, 2024

  1. Merge branch 'dev' of https://github.com/nf-core/mag into nf-core-tem… 

    …plate-merge-2.12
    @CarsonJM
    CarsonJM committed Feb 1, 2024
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  2. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Feb 1, 2024
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  3. Fixed linting errors

    @CarsonJM
    CarsonJM committed Feb 1, 2024
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  4. Add warning if no GTDB results because no contigs pass filter

    @jfy133
    jfy133 committed Feb 1, 2024
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  5. Add changelog and missing changelog entry

    @jfy133
    jfy133 committed Feb 1, 2024
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  6. Update MultiQC to 1.19 start tweaking confgig

    @jfy133
    jfy133 committed Feb 1, 2024
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  7. Fixed linting in usage.md

    @CarsonJM
    CarsonJM committed Feb 1, 2024
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  8. Fixed docker.runOptions merge error

    @CarsonJM
    CarsonJM committed Feb 1, 2024
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  9. Update CHANGELOG.md

    @jfy133
    jfy133 authored Feb 1, 2024
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  10. Tweak order of MultiQC sections to better match workflow order

    @jfy133
    jfy133 committed Feb 1, 2024
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  11. Fix author

    @jfy133
    jfy133 committed Feb 1, 2024
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  12. Merge pull request #562 from maxibor/add_cat_2_summary 

    Add CAT summary into the global `bin_summary`
    @jfy133
    jfy133 authored Feb 1, 2024
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  13. Merge branch 'dev' into warn-when-gtdb-filter-empty

    @jfy133
    jfy133 authored Feb 1, 2024
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  14. Update .nf-core.yml

    @jfy133
    jfy133 authored Feb 1, 2024
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  15. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Feb 1, 2024
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  16. Merge pull request #563 from nf-core/nf-core-template-merge-2.12 

    Important! Template update for nf-core/tools v2.12
    @jfy133
    jfy133 authored Feb 1, 2024
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  17. Merge remote-tracking branch 'origin/dev' into warn-when-gtdb-filter-… 

    …empty
    @jfy133
    jfy133 committed Feb 1, 2024
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  18. Merge remote-tracking branch 'origin/dev' into multiqc-tweak

    @jfy133
    jfy133 committed Feb 1, 2024
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  19. Merge pull request #565 from nf-core/warn-when-gtdb-filter-empty 

    Add warning GTDB-TK results will be empty if no contigs pass completeness filter
    @jfy133
    jfy133 authored Feb 1, 2024
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  20. Merge pull request #566 from nf-core/multiqc-tweak 

    Tweak order of MultiQC sections to better match workflow
    @CarsonJM
    CarsonJM authored Feb 1, 2024
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Commits on Feb 2, 2024

  1. Update CHANGELOG and bump version for reelase

    @jfy133
    jfy133 committed Feb 2, 2024
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  2. Typo fix

    @jfy133
    jfy133 committed Feb 2, 2024
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  3. Merge pull request #567 from nf-core/bump-version-for-reelase 

    Bump version for 2.5.2 reelase
    @jfy133
    jfy133 authored Feb 2, 2024
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  4. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Feb 2, 2024
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  5. Update devcontainer.json for linting

    @jfy133
    jfy133 authored Feb 2, 2024
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  6. Merge pull request #569 from nf-core/jfy133-patch-1 

    Update devcontainer.json for linting
    @jfy133
    jfy133 authored Feb 2, 2024
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  7. Add newer major contributors

    @jfy133
    jfy133 authored Feb 2, 2024
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  8. Merge pull request #571 from nf-core/jfy133-patch-1 

    Add newer major contributors
    @jfy133
    jfy133 authored Feb 2, 2024
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