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Bin QC Improvements #707

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Bin QC Improvements #707

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Commits on Oct 27, 2024

  1. feat: Migrate from CheckM to CheckM2 

    - Update modules
- Update integration in mag and with other tools (bin_summary, gtdb-tk)
- Update test
- Update schema
    @dialvarezs
    dialvarezs committed Oct 27, 2024
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  2. fix: Bring back CheckM

    @dialvarezs
    dialvarezs committed Oct 27, 2024
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  3. fix: One more thing

    @dialvarezs
    dialvarezs committed Oct 27, 2024
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  4. fix: Linting

    @dialvarezs
    dialvarezs committed Oct 27, 2024
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  5. fix: Option and checks in bin summary script

    @dialvarezs
    dialvarezs committed Oct 27, 2024
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  6. Fix: missing import

    @dialvarezs
    dialvarezs committed Oct 27, 2024
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Commits on Oct 28, 2024

  1. docs: Output, changelog and citation for CheckM2

    @dialvarezs
    dialvarezs committed Oct 28, 2024
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  2. docs: readme

    @dialvarezs
    dialvarezs committed Oct 28, 2024
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  3. Merge remote-tracking branch 'upstream/dev' into dev-checkm2

    @dialvarezs
    dialvarezs committed Oct 28, 2024
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  4. docs: Update readme

    @dialvarezs
    dialvarezs committed Oct 28, 2024
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  5. refactor: Merge checkm and checkm2 subworkflows in a single one 

    Also, simplify bin_summary regarding bin qc
    @dialvarezs
    dialvarezs committed Oct 28, 2024
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  6. fix: Restore mistakenly deleted code

    @dialvarezs
    dialvarezs committed Oct 28, 2024
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Commits on Oct 31, 2024

  1. Bin QC workflow

    @dialvarezs
    dialvarezs committed Oct 31, 2024
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  2. Merge remote-tracking branch 'upstream/dev' into dev-checkm2

    @dialvarezs
    dialvarezs committed Oct 31, 2024
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  3. Cleanup

    @dialvarezs
    dialvarezs committed Oct 31, 2024
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  4. Final touches

    @dialvarezs
    dialvarezs committed Oct 31, 2024
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Commits on Nov 1, 2024

  1. Integrate GUNC in BIN_QC subworkflow

    @dialvarezs
    dialvarezs committed Nov 1, 2024
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  2. Code style improvements

    @dialvarezs
    dialvarezs committed Nov 1, 2024
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Commits on Nov 25, 2024

  1. Merge branch 'dev' into dev-checkm2

    @jfy133
    jfy133 authored Nov 25, 2024
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Commits on Nov 27, 2024

  1. Address several review comments

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  2. Update modules

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  3. Make binqc_tool an input for BIN_SUMMARY

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  4. Move bin qc database setup to the subworkflow

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  5. Fix

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  6. Remove another it

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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  7. Remove checkm/checkm2 ci tests

    @dialvarezs
    dialvarezs committed Nov 27, 2024
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Commits on Nov 28, 2024

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

    @dialvarezs
    dialvarezs committed Nov 28, 2024
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  2. Don't flatten bins for GUNC

    @dialvarezs
    dialvarezs committed Nov 28, 2024
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  3. Update changelog

    @dialvarezs
    dialvarezs committed Nov 28, 2024
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  4. Emit bash version on busco_save_download

    @dialvarezs
    dialvarezs committed Nov 28, 2024
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  5. Fix declaration

    @dialvarezs
    dialvarezs committed Nov 28, 2024
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