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Split deepvariant 3#6172

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maxulysse merged 22 commits intonf-core:masternf-core/modules:masterfrom fa2k:split-deepvariant-3fa2k/modules:split-deepvariant-3Copy head branch name to clipboardSep 12, 2024

+2,241-200

Commits

Commits on Aug 8, 2024

• Move DeepVariant into a subcommand module rundeepvariant, preparing for split modules

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Commits on Aug 9, 2024

• Add a split DeepVariant workflow with individual processes for each step

  fa2k

  committed
  7328e6b

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• Remove hash unique ID and fix input structure issue

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  committed
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Commits on Aug 13, 2024

• Fixes for call_variants outputing sharded file

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• Fix test

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Commits on Aug 15, 2024

• Remove --channels insert_size, which is only applicable for short read

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• Replace the model type value input with ext.args config

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Commits on Aug 16, 2024

• Fix tests: should run twice for two samples in input channel

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Commits on Aug 29, 2024

• Merge remote-tracking branch 'upstream/master' into split-deepvariant-3

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• Fix linting issues and input channel description

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Commits on Aug 30, 2024

• Merge branch 'master' into split-deepvariant-3

  fellen31

  authored
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Commits on Sep 4, 2024

• Fix formatting of md files

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  fa2k

  and

  fellen31

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• Corrections / imrpovements from @fellen31 review

  fa2k

  committed
  dfb2c39

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• Merge remote-tracking branch 'upstream/master' into split-deepvariant-3

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  committed
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• Check tfrecord file names

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Commits on Sep 6, 2024

• Merge branch 'master' into split-deepvariant-3

  maxulysse

  authored
  aacec0d

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• Merge remote-tracking branch 'upstream/master' into split-deepvariant-3

  fa2k

  committed
  baa0e17

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• Updating conda skipping options, because the paths have changed

  fa2k

  committed
  f2c1ea8

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• Add deprecation warning for top-level process and test for the deprecated process

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  committed
  fdf1d21

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• also skip conda for the new deprecated module

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  committed
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Commits on Sep 9, 2024

• Merge branch 'master' into split-deepvariant-3

  maxulysse

  authored
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Commits on Sep 12, 2024

• Merge branch 'master' into split-deepvariant-3

  maxulysse

  authored
  5ae3d01

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