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Template merge#106

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zachary-foster merged 30 commits intonf-core:devnf-core/pathogensurveillance:devfrom grunwaldlab:template_mergegrunwaldlab/pathogensurveillance:template_mergeCopy head branch name to clipboardOct 30, 2024

+5,182-2,797

Commits

Commits on May 8, 2024

• Template update for nf-core/tools version 2.14.0

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  35c4c48

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Commits on May 9, 2024

• Template update for nf-core/tools version 2.14.1

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Commits on Oct 8, 2024

• Template update for nf-core/tools version 3.0.0

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Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

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Commits on Oct 11, 2024

• Template update for nf-core/tools version 3.0.2

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  240c46a

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Commits on Oct 21, 2024

• replace tabs with spaces

  

  Zachary Foster

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Commits on Oct 25, 2024

• fix readme

  

  Zachary Foster

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  a6375a2

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• convert " to ' in input CSV and allow for user-defined columns in the reference metadata

  

  Zachary Foster

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  fd9dc87

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• redo mixed test dataset

  

  Zachary Foster

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  64578f7

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• refactored the genome assembly code to be more flexible with multiple assembliers

  

  Zachary Foster

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• sketch comparison is now done on assemblies

  

  Zachary Foster

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  9e1c2f2

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• fix bugs

  

  Zachary Foster

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  2c35fcb

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• stop duplicated bakta runs

  

  Zachary Foster

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  03df25c

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• more bug fixes

  

  Zachary Foster

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  4e46e83

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• remove two cols from complex test dataset

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• remove col with no header from test data file

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  33c84dc

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• fixed trace report not being saved

  

  Zachary Foster

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  51640c8

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• use spades for shortread euakaryotes

  

  Zachary Foster

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Commits on Oct 26, 2024

• warn if a sample cannot be assembled

  

  Zachary Foster

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  e4a086c

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• prefer references with standard binomial names

  

  Zachary Foster

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• added option to only use references with standard latin bionomial names

  

  Zachary Foster

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Commits on Oct 28, 2024

• switch to pacbio-raw for flye assembly

  

  Zachary Foster

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  4e46566

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• fix bug where single end Illumia reads were causing fastp to fail

  

  Zachary Foster

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Commits on Oct 29, 2024

• make assembliers try with a little RAM, but try with much more if they fail

  

  Zachary Foster

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  63ffddb

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• tuning assembler resource settings

  

  Zachary Foster

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  50a97d4

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• try to make spades faster

  

  Zachary Foster

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  52acc37

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• merge

  

  Zachary Foster

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  e6a9af8

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

  Zachary Foster

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• resolved merge conflicts, but nothing else yet

  

  Zachary Foster

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  e639e7d

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Commits on Oct 30, 2024

• fixed bugs caused by merge

  

  Zachary Foster

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