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Fix GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test #1173

Merged
merged 27 commits into from
Aug 16, 2023
Merged

Fix GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test #1173

merged 27 commits into from
Aug 16, 2023

Commits on Aug 5, 2023

  1. simplify hc filtering logic

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  2. pull params out of sw

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  3. update changelog

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  4. only join on file name to make this more stable

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  5. add stub tests

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  6. rename test

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  7. add tags

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  8. revert local changes to csv

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  9. update modules

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  10. fix duplicate entries in vcf

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  11. update changelof

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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  12. fix stub test

    @FriederikeHanssen
    FriederikeHanssen committed Aug 5, 2023
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Commits on Aug 6, 2023

  1. test fix for samplesheet

    @FriederikeHanssen
    FriederikeHanssen committed Aug 6, 2023
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  2. add view for debugging [skip actions]

    @FriederikeHanssen
    FriederikeHanssen committed Aug 6, 2023
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  3. add intervals name to avoid random joining

    @FriederikeHanssen
    FriederikeHanssen committed Aug 6, 2023
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  4. add comments

    @FriederikeHanssen
    FriederikeHanssen committed Aug 6, 2023
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Commits on Aug 15, 2023

  1. Merge branch 'dev' into refactor_hc

    @FriederikeHanssen
    FriederikeHanssen committed Aug 15, 2023
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  2. remove docker tag

    @FriederikeHanssen
    FriederikeHanssen committed Aug 15, 2023
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  3. Merge branch 'dev' into refactor_hc

    @FriederikeHanssen
    FriederikeHanssen committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. add ugly channel magic beast

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  2. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Aug 16, 2023
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  3. add missing keys

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  4. Merge remote-tracking branch 'origin/refactor_hc' into refactor_hc

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  5. update md5sums

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  6. simplify logic + fix output paths

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  7. fix output paths

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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  8. remove view statement

    @FriederikeHanssen
    FriederikeHanssen committed Aug 16, 2023
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