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Refactor #1151

Merged
merged 22 commits into from
Jul 12, 2023
Merged

Refactor #1151

merged 22 commits into from
Jul 12, 2023

Commits on Jul 10, 2023

  1. indent things, clean up, add comments, consolidate

    @FriederikeHanssen
    FriederikeHanssen committed Jul 10, 2023
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  2. refactor post vc steps to prepare for varlociraptor

    @FriederikeHanssen
    FriederikeHanssen committed Jul 10, 2023
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  3. fix import paths

    @FriederikeHanssen
    FriederikeHanssen committed Jul 10, 2023
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  4. get rid of WARN: There's no process matching config selector

    @FriederikeHanssen
    FriederikeHanssen committed Jul 10, 2023
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  5. add post vc back in

    @FriederikeHanssen
    FriederikeHanssen committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. test md and sentieon separately

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  2. fix input channel cardinality for fgbio

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  3. fix naming

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  4. fix more bad spacing, typos

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  5. update sw map with concatenate, move type description

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  6. simplify test config

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  7. simplify test config

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  8. update PR ID

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  9. remove gvcf vcfs from csv for restart

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  10. simplify everything

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  11. add spaces for prettyness

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  12. fix variable name

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  13. remove empty channel

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  14. spread out gatk md and sentieon dedup more

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  15. update md5sums since csv don't contain gvcf files

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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  16. add selector to get controlfreec tests to pass

    @FriederikeHanssen
    FriederikeHanssen committed Jul 11, 2023
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Commits on Jul 12, 2023

  1. need to keep wild card declaration to ensure precendence

    @FriederikeHanssen
    FriederikeHanssen committed Jul 12, 2023
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