Code

Work on testing pipeline#5

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Merged

dfornika merged 24 commits intomainBCCDC-PHL/fluviewer-nf:mainfrom testing-pipeline-continuedBCCDC-PHL/fluviewer-nf:testing-pipeline-continuedCopy head branch name to clipboardJun 7, 2024

+410-285

Commits

Commits on Jun 5, 2024

• Work on testing pipeline

  dfornika

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  f7b23d2

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• troubleshooting provenance generation

  dfornika

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  1385c31

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• Add testing workflow

  dfornika

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  e048c1d

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• make conda (and mamba?) available when running the pipeline

  dfornika

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  953b255

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• fix home dir path

  dfornika

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  ecb4da1

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• add another sample to simulate, this one directly from FluViewer db

  dfornika

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  11ed458

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• Add another sample to simulate from FluViewer db

  dfornika

  committed
  ac72d6d

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• Build multi-segment ref to simulate reads from

  dfornika

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  f862e72

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• touching up provenance

  dfornika

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  aebf1ca

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• tidying up

  dfornika

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  5b895e2

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• rename snp_calling module

  dfornika

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  da113f7

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• typo geoflu -> genoflu

  dfornika

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  e69f339

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• small fixes

  dfornika

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  9e42cb6

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• Disable nextflow v23 test temporarily

  dfornika

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  ff724b8

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• Restore fluviewer conda env directive

  dfornika

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  fc671b7

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• updates

  dfornika

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  479ed7d

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• organize environments

  dfornika

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  232476c

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• fix sed cmd

  dfornika

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• fix env path

  dfornika

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• updates

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  fd10afb

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• update

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Commits on Jun 6, 2024

• collect nextflow log

  dfornika

  committed
  ea26a15

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• collect nextflow log

  dfornika

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  ea6bf48

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• tidy up nextclade provenance

  dfornika

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  458dd7b

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