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Release PR for 3.0 #616

Merged
merged 57 commits into from
May 13, 2024
Merged

Release PR for 3.0 #616

merged 57 commits into from
May 13, 2024

Commits on Feb 12, 2024

  1. Fix rendering of markdown badges

    @jfy133
    jfy133 authored Feb 12, 2024
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  2. Post-release version bump

    @jfy133
    jfy133 committed Feb 12, 2024
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  3. Merge pull request #586 from nf-core/post-release-version-bump 

    Post-release version bump
    @jfy133
    jfy133 authored Feb 12, 2024
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Commits on Feb 16, 2024

  1. Turn on Krona in base test

    @jfy133
    jfy133 committed Feb 16, 2024
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  2. Add CONCOCT test profile and tweak test_nothing metadata

    @jfy133
    jfy133 committed Feb 16, 2024
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  3. Add CONCOCT test profile

    @jfy133
    jfy133 committed Feb 16, 2024
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  4. Merge pull request #591 from nf-core/new-configs 

    Add test configs for krona and concoct
    @CarsonJM
    CarsonJM authored Feb 16, 2024
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  5. Merge branch 'nf-core:master' into single-end-config

    @CarsonJM
    CarsonJM authored Feb 16, 2024
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  6. Added single_end test

    @CarsonJM
    CarsonJM committed Feb 16, 2024
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  7. Merge branch 'single-end-config' of https://github.com/CarsonJM/mag i… 

    …nto single-end-config
    @CarsonJM
    CarsonJM committed Feb 16, 2024
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  8. Merge branch 'dev' into single-end-config

    @CarsonJM
    CarsonJM authored Feb 16, 2024
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  9. [automated] Fix code linting

    @nf-core-bot
    nf-core-bot committed Feb 16, 2024
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  10. Merge pull request #593 from CarsonJM/single-end-config 

    Created single end test
    @CarsonJM
    CarsonJM authored Feb 16, 2024
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Commits on Feb 20, 2024

  1. Template update for nf-core/tools version 2.13

    @nf-core-bot
    nf-core-bot committed Feb 20, 2024
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Commits on Feb 29, 2024

  1. Template update for nf-core/tools version 2.13.1

    @nf-core-bot
    nf-core-bot committed Feb 29, 2024
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Commits on Mar 13, 2024

  1. feat: allow adna co-binning

    @maxibor
    maxibor committed Mar 13, 2024
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  2. chore: update changelog

    @maxibor
    maxibor committed Mar 13, 2024
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Commits on Mar 26, 2024

  1. Fix gtdbtk classifywf crash when mashdb given

    @jfy133
    jfy133 committed Mar 26, 2024
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  2. improve changelgo

    @jfy133
    jfy133 committed Mar 26, 2024
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  3. Merge branch 'dev' into nf-core-template-merge-2.13.1 [EXPECT TO FAIL]

    @jfy133
    jfy133 committed Mar 26, 2024
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  4. Merge pull request #608 from nf-core/update-gtdbtk-classifwy 

    Update gtdbtk classifywf so doesn't break when mashdb given
    @jfy133
    jfy133 authored Mar 26, 2024
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  5. Get basic input samplesheet validation in, however need to check from… 

    …Samplesheet/map function in utils_nfcore_mag_pipeline
    @jfy133
    jfy133 committed Mar 26, 2024
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  6. Get pipeline seemingly running again

    @jfy133
    jfy133 committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. Re-add single end as can't mix the two in one run

    @jfy133
    jfy133 committed Mar 27, 2024
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  2. Get SR tests working, start adding assmebly

    @jfy133
    jfy133 committed Mar 27, 2024
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  3. Re-add missing single end test

    @jfy133
    jfy133 committed Mar 27, 2024
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  4. Re-add single-end test config

    @jfy133
    jfy133 committed Mar 27, 2024
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Commits on Apr 18, 2024

  1. Apply suggestions from code review

    @jfy133
    jfy133 authored Apr 18, 2024
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Commits on Apr 19, 2024

  1. All --input validation checks working

    @jfy133
    jfy133 committed Apr 19, 2024
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  2. Move all input parameter code to utils_nfcore_mag subworkflow

    @jfy133
    jfy133 committed Apr 19, 2024
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  3. Merge pull request #602 from maxibor/adna_binning_group 

    feat: allow adna co-binning
    @jfy133
    jfy133 authored Apr 19, 2024
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  4. Complete validation transfer

    @jfy133
    jfy133 committed Apr 19, 2024
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  5. Merge branch 'dev' of github.com:nf-core/mag into nf-core-template-me… 

    …rge-2.13.1
    @jfy133
    jfy133 committed Apr 19, 2024
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  6. update CHANGELOG

    @jfy133
    jfy133 committed Apr 19, 2024
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  7. Update nextflow_schema.json

    @jfy133
    jfy133 authored Apr 19, 2024
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  8. Apply suggestions from code review

    @jfy133
    jfy133 authored Apr 19, 2024
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  9. Update nextflow_schema.json

    @jfy133
    jfy133 authored Apr 19, 2024
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  10. Remove duplication

    @jfy133
    jfy133 committed Apr 19, 2024
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  11. Merge branch 'nf-core-template-merge-2.13.1' of github.com:nf-core/ma… 

    …g into nf-core-template-merge-2.13.1
    @jfy133
    jfy133 committed Apr 19, 2024
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Commits on Apr 24, 2024

  1. Fix validateInputSamplesheet usage

    @jfy133
    jfy133 committed Apr 24, 2024
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Commits on May 6, 2024

  1. Fix zenodo ID

    @jfy133
    jfy133 committed May 6, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @jfy133 @maxulysse
    jfy133 and maxulysse authored May 6, 2024
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  3. Fix linting error

    @jfy133
    jfy133 committed May 6, 2024
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  4. Merge branch 'nf-core-template-merge-2.13.1' of github.com:nf-core/ma… 

    …g into nf-core-template-merge-2.13.1
    @jfy133
    jfy133 committed May 6, 2024
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  5. Fix gunzipping of pre-supplied assmeblies

    @jfy133
    jfy133 committed May 6, 2024
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  6. Merge pull request #599 from nf-core/nf-core-template-merge-2.13.1 

    Important! Template update for nf-core/tools v2.13.1
    @jfy133
    jfy133 authored May 6, 2024
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Commits on May 8, 2024

  1. Template update for nf-core/tools version 2.14.0

    @nf-core-bot
    nf-core-bot committed May 8, 2024
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Commits on May 9, 2024

  1. Template update for nf-core/tools version 2.14.1

    @nf-core-bot
    nf-core-bot committed May 9, 2024
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Commits on May 10, 2024

  1. Merge branch 'dev' into nf-core-template-merge-2.14.1

    @jfy133
    jfy133 authored May 10, 2024
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  2. Update all test data to new system

    @jfy133
    jfy133 committed May 10, 2024
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  3. Merge pull request #614 from nf-core/nf-core-template-merge-2.14.1 

    Important! Template update for nf-core/tools v2.14.1
    @jfy133
    jfy133 authored May 10, 2024
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  4. Add new logo!

    @jfy133
    jfy133 committed May 10, 2024
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  5. Merge pull request #615 from nf-core/new-logo 

    Add new logo
    @jfy133
    jfy133 authored May 10, 2024
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  6. Update versions

    @jfy133
    jfy133 committed May 10, 2024
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  7. Fix module JSON

    @jfy133
    jfy133 committed May 10, 2024
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  8. Harshil alignment

    @jfy133
    jfy133 committed May 10, 2024
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Commits on May 13, 2024

  1. Update workflows/mag.nf

    @jfy133
    jfy133 authored May 13, 2024
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