Code

Bin QC Improvements#707

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dialvarezs merged 38 commits intonf-core:devnf-core/mag:devfrom dialvarezs:dev-checkm2dialvarezs/mag:dev-checkm2Copy head branch name to clipboardDec 13, 2024

+1,846-566

Commits

Commits on Oct 27, 2024

• feat: Migrate from CheckM to CheckM2

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• fix: Bring back CheckM

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  ca2f97b

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• fix: One more thing

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  05e3393

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• fix: Linting

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  3e49dbf

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• fix: Option and checks in bin summary script

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  b1b6518

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• Fix: missing import

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Commits on Oct 28, 2024

• docs: Output, changelog and citation for CheckM2

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• docs: readme

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• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

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• docs: Update readme

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  3da7441

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• refactor: Merge checkm and checkm2 subworkflows in a single one

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• fix: Restore mistakenly deleted code

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Commits on Oct 31, 2024

• Bin QC workflow

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  76dac5c

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• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

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  0ebab07

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• Cleanup

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• Final touches

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Commits on Nov 1, 2024

• Integrate GUNC in BIN_QC subworkflow

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• Code style improvements

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Commits on Nov 25, 2024

• Merge branch 'dev' into dev-checkm2

  jfy133

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Commits on Nov 27, 2024

• Address several review comments

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  3158c52

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• Update modules

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• Make binqc_tool an input for BIN_SUMMARY

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• Move bin qc database setup to the subworkflow

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  bcae7f9

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• Fix

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• Remove another it

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• Remove checkm/checkm2 ci tests

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Commits on Nov 28, 2024

• gtdbtk: add check when params.busco_db is not defined

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  4ecd36f

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• Don't flatten bins for GUNC

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  1cf1da7

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• Update changelog

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• Emit bash version on busco_save_download

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  a079596

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• Fix declaration

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  80641b0

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Commits on Dec 1, 2024

• Update checkm/qa module

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  4b084b1

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Commits on Dec 5, 2024

• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

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  f75e9c4

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• Handle skip_binqc properly

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Commits on Dec 11, 2024

• Address review comments

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  3a38a37

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Commits on Dec 13, 2024

• Merge branch 'dev' into dev-checkm2

  jfy133

  authored
  009abd1

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• Update tests to integrate CheckM and CheckM2

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  a2afa5e

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• Fix for when checkm is not run for some bins

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