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Fix Mutect2 #544

Merged
merged 19 commits into from
May 16, 2022
Merged

Fix Mutect2 #544

merged 19 commits into from
May 16, 2022

Commits on May 13, 2022

  1. nf-core modules update -all

    @FriederikeHanssen
    FriederikeHanssen committed May 13, 2022
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  2. Mutect2 tumor only is back

    @FriederikeHanssen
    FriederikeHanssen committed May 13, 2022
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  3. missing bracket

    @FriederikeHanssen
    FriederikeHanssen committed May 13, 2022
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  4. Add readgroup update also for mutect implementation

    @FriederikeHanssen
    FriederikeHanssen committed May 13, 2022
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Commits on May 15, 2022

  1. Mutect Paried working

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  2. Foramtting

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  3. Add custom --name to mutect2 test

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  4. Add mutect2/no_intervals warning

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  5. Add mutect2/no_intervals warning

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  6. fix test config path

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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  7. add variantcaller filed for annotation

    @FriederikeHanssen
    FriederikeHanssen committed May 15, 2022
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Commits on May 16, 2022

  1. Keep filtered vcf and use them for annotation

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  2. Keep filtered vcf and use them for annotation

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  3. Merge remote-tracking branch 'origin/fix_mutect2' into fix_mutect2

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  4. Publish pileuptables to tumor_vs_normal results dir

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  5. fix output path

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  6. update modules

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  7. Add error message if mutect2 and no_intervals is used. Test for it

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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  8. Update changelog

    @FriederikeHanssen
    FriederikeHanssen committed May 16, 2022
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