Code

Refactor#1151

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Merged

FriederikeHanssen merged 22 commits intodevnf-core/sarek:devfrom refactornf-core/sarek:refactorCopy head branch name to clipboardJul 12, 2023

+658-513

Commits

Commits on Jul 10, 2023

• indent things, clean up, add comments, consolidate

  FriederikeHanssen

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  7ba9311

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• refactor post vc steps to prepare for varlociraptor

  FriederikeHanssen

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  fe1c506

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• fix import paths

  FriederikeHanssen

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  d8e6fe7

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• get rid of WARN: There's no process matching config selector

  FriederikeHanssen

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  e80d157

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• add post vc back in

  FriederikeHanssen

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  be9786f

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Commits on Jul 11, 2023

• test md and sentieon separately

  FriederikeHanssen

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  ce4a924

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• fix input channel cardinality for fgbio

  FriederikeHanssen

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  000de54

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• fix naming

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  483fd18

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• fix more bad spacing, typos

  FriederikeHanssen

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  3b53b05

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• update sw map with concatenate, move type description

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  7efdf76

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• simplify test config

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  764e09d

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• simplify test config

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  7eba720

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• update PR ID

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  c36a726

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• remove gvcf vcfs from csv for restart

  FriederikeHanssen

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  81dde8c

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• simplify everything

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  fc203ac

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• add spaces for prettyness

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  2430c9a

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• fix variable name

  FriederikeHanssen

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  f5e3aac

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• remove empty channel

  FriederikeHanssen

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  10249ca

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• spread out gatk md and sentieon dedup more

  FriederikeHanssen

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  6584e32

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• update md5sums since csv don't contain gvcf files

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  46ff810

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• add selector to get controlfreec tests to pass

  FriederikeHanssen

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  0d8999b

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Commits on Jul 12, 2023

• need to keep wild card declaration to ensure precendence

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  bf43387

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