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feat: Add gene order subworkflow #131

Merged
merged 34 commits into from
Nov 12, 2023
Merged

feat: Add gene order subworkflow #131

merged 34 commits into from
Nov 12, 2023

Commits on Jun 9, 2023

  1. feat: Begin building gene order subwf

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    jvfe committed Jun 9, 2023
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Commits on Jun 14, 2023

  1. feat: Add alignment step to pipeline

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    jvfe committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. Merge branch 'master' into gene-order-workflow 

    * master:
  refactor: Use 'samplesheet' for alignment concat (#130)
  refactor: Remove phispy info from report (#128)
  feat: Automate phylogenomic analysis from ppanggolin outs (#127)
    @jvfe
    jvfe committed Jun 15, 2023
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  2. refactor: Make extraction.py accept list of files instead of dirs

    @jvfe
    jvfe committed Jun 15, 2023
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  3. refactor: Add all extraction output files as module output

    @jvfe
    jvfe committed Jun 15, 2023
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  4. feat: Begin building clustering.nf

    @jvfe
    jvfe committed Jun 15, 2023
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  5. chore: Add latest changes from main repo

    @jvfe
    jvfe committed Jun 15, 2023
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  6. feat: Use all possible combinations for alignment

    @jvfe
    jvfe committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. Try fixing clustering

    @jvfe
    jvfe committed Jun 16, 2023
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Commits on Jun 20, 2023

  1. fix: Add upstream fixes from Julia

    @jvfe
    jvfe committed Jun 20, 2023
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  2. feat: Add gene order modules to output dir

    @jvfe
    jvfe committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. fix: Emit correct outputs in clustering.nf

    @jvfe
    jvfe committed Jun 21, 2023
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Commits on Jun 23, 2023

  1. refactor: Make extraction output have _temp suffix

    @jvfe
    jvfe committed Jun 23, 2023
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  2. refactor: Change visualization.py to use plotly CDN

    @jvfe
    jvfe committed Jun 23, 2023
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  3. feat: Add --plot_clustering to optionally make HTML files

    @jvfe
    jvfe committed Jun 23, 2023
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  4. chore: Add Gene Order params to schema

    @jvfe
    jvfe committed Jun 23, 2023
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  5. refactor: Remove original temp JSON file from output

    @jvfe
    jvfe committed Jun 23, 2023
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Commits on Jun 27, 2023

  1. Merge branch 'master' into gene-order-workflow 

    * master:
  fix: Change create_report back to high_memory
  refactor: Use collect output in filter/add_column and optional report (#139)
  refactor: Increase default reqs for ppanggolin and create_report (#137)
  feat: Check sample ID validity with Annotation input check (#136)
  feat: Add annotation tools param (#134)
  docs: Add new ARETE logo (#135)
  feat: Add param to skip the pan/phylo subwf (#132)
    @jvfe
    jvfe committed Jun 27, 2023
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  2. chore: Add Julia's changes from the latest update

    @jvfe
    jvfe committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. feat: Add gene order subwf to ARETE

    @jvfe
    jvfe committed Jun 28, 2023
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  2. refactor: Swap containers to docker ones

    @jvfe
    jvfe committed Jun 28, 2023
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  3. refactor: Update singularity image

    @jvfe
    jvfe committed Jun 28, 2023
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  4. Revert "refactor: Update singularity image" 

    This reverts commit 5382f39.
    @jvfe
    jvfe committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. refactor: Change skip to run

    @jvfe
    jvfe committed Jun 29, 2023
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  2. fix: Change indenting

    @jvfe
    jvfe committed Jun 29, 2023
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  3. test: Add test for gene order subwf

    @jvfe
    jvfe committed Jun 29, 2023
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Commits on Oct 11, 2023

  1. refactor: Fix paths

    @jvfe
    jvfe committed Oct 11, 2023
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  2. ci: Skip gene-order

    @jvfe
    jvfe committed Oct 11, 2023
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Commits on Oct 14, 2023

  1. feat: Add changes from cba3ca4 and 9a5a9a

    @jvfe
    jvfe committed Oct 14, 2023
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  2. style: Add black to other bin/ files

    @jvfe
    jvfe committed Oct 14, 2023
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Commits on Oct 15, 2023

  1. refactor: Remove gene order HTML template from code

    @jvfe
    jvfe committed Oct 15, 2023
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Commits on Nov 10, 2023

  1. Merge branch 'master' into gene-order-workflow 

    * master:
  feat: Add recombination entry (#175)
  docs: Add evolCCM usage documentation
  feat: Add evolCCM entry (#174)
  docs: Update rSPR outputs (#173)
  fix: Stop ppanggolin msa from altering input file (#172)
  feat: Add rspr entry (#171)
  refactor: Ignore time reached error in rspr_exact (#170)
    @jvfe
    jvfe committed Nov 10, 2023
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  2. fix: Remove mentions of html-template

    @jvfe
    jvfe committed Nov 10, 2023
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Commits on Nov 12, 2023

  1. docs: Add gene order to output and params

    @jvfe
    jvfe committed Nov 12, 2023
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