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Enhancement snakemake analysis #472

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Enhancement snakemake analysis #472

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Commits on Jun 7, 2024

  1. testing snakemake functionality

    @adamcantor22
    adamcantor22 committed Jun 7, 2024
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  2. anova and permanova metric-independent

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    adamcantor22 committed Jun 7, 2024
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Commits on Jun 11, 2024

  1. restructuring

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    adamcantor22 committed Jun 11, 2024
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Commits on Jun 14, 2024

  1. starting new analysis structure

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    adamcantor22 committed Jun 14, 2024
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  2. seaborn install

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    adamcantor22 committed Jun 14, 2024
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  3. seaborn install

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    adamcantor22 committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. analysis setup and pipeline working

    @adamcantor22
    adamcantor22 committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. replace tool_type with workflow_type. REMEMBER TO UPDATE MONGODB WITH… 

    … THIS NAME CHANGE
    @adamcantor22
    adamcantor22 committed Jun 18, 2024
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Commits on Jun 24, 2024

  1. more generalizable workflow setup

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    adamcantor22 committed Jun 24, 2024
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  2. folder restructuring

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    adamcantor22 committed Jun 24, 2024
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Commits on Jul 10, 2024

  1. lefse workflow

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    adamcantor22 committed Jul 10, 2024
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  2. lefse workflow file

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    adamcantor22 committed Jul 10, 2024
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Commits on Jul 12, 2024

  1. lefse pipeline and modes

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    adamcantor22 committed Jul 12, 2024
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Commits on Jul 16, 2024

  1. lefse plots

    @adamcantor22
    adamcantor22 committed Jul 16, 2024
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  2. versions

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    adamcantor22 committed Jul 16, 2024
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  3. versions

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    adamcantor22 committed Jul 16, 2024
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  4. versions

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  5. versions

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Commits on Jul 17, 2024

  1. more versions

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    adamcantor22 committed Jul 17, 2024
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  2. workflow updates

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    adamcantor22 committed Jul 17, 2024
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  3. the conda environments work now, although not due to this code change

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    adamcantor22 committed Jul 17, 2024
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  4. remove testing of old tools

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    adamcantor22 committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. lefse analysis working as jobfile

    @adamcantor22
    adamcantor22 committed Jul 18, 2024
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  2. reorder module load

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    adamcantor22 committed Jul 18, 2024
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  3. standard pipeline working partial cases

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    adamcantor22 committed Jul 18, 2024
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  4. working on old tests

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    adamcantor22 committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. working old tests

    @adamcantor22
    adamcantor22 committed Jul 19, 2024
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  2. add dummy classifier to tests

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    adamcantor22 committed Jul 19, 2024
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  3. put it in the right spot

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    adamcantor22 committed Jul 19, 2024
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  4. don't check process length if none found

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    adamcantor22 committed Jul 19, 2024
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  5. increase how much time is spent checking current processes due to lon… 

    …ger times on github
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  6. Actually do that instead of making an infinite loop

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    adamcantor22 authored Jul 19, 2024
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  7. Cleanup pipe after test_a

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    adamcantor22 authored Jul 19, 2024
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  8. Typo

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    adamcantor22 authored Jul 19, 2024
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  9. Debugging

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Commits on Jul 22, 2024

  1. new method checking current procs

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    adamcantor22 committed Jul 22, 2024
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  2. debugging current procs

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    adamcantor22 committed Jul 22, 2024
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  3. show logger

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    adamcantor22 committed Jul 22, 2024
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  4. show logger on failure

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    adamcantor22 committed Jul 22, 2024
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  5. use existing action instead of echo/cat

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    adamcantor22 committed Jul 22, 2024
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  6. debug

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    adamcantor22 committed Jul 22, 2024
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  7. remove unimportant logs

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    adamcantor22 committed Jul 22, 2024
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  8. swap order

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    adamcantor22 committed Jul 22, 2024
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  9. use command

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    adamcantor22 committed Jul 22, 2024
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  10. correct id

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    adamcantor22 committed Jul 22, 2024
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  11. try action fork

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    adamcantor22 committed Jul 22, 2024
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  12. fixing analysis process

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    adamcantor22 committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. debugging

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    adamcantor22 committed Jul 23, 2024
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  2. pad runtimes

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    adamcantor22 committed Jul 23, 2024
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  3. revert permissions

    @adamcantor22
    adamcantor22 committed Jul 23, 2024
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  4. updating jupyter env, this is not a good system

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    adamcantor22 committed Jul 23, 2024
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  5. updating pandas

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  6. more versions

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    adamcantor22 committed Jul 23, 2024
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  7. removing summaries testing, not implemented for new features

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    adamcantor22 committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. brackets around categories

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  2. codecov v4

    @adamcantor22
    adamcantor22 committed Jul 24, 2024
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  3. better lefse rules

    @adamcantor22
    adamcantor22 committed Jul 24, 2024
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  4. tools in manifest

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    adamcantor22 committed Jul 24, 2024
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  5. correct dirs

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    adamcantor22 committed Jul 24, 2024
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  6. token

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    adamcantor22 committed Jul 24, 2024
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  7. still create empty pdf

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    adamcantor22 committed Jul 24, 2024
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  8. correct else

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  9. lefse readability

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    adamcantor22 committed Jul 24, 2024
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  10. Merge branch 'Enhancement-SnakemakeAnalysis' of https://github.com/cl… 

    …emente-lab/mmeds-meta into Enhancement-SnakemakeAnalysis
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Commits on Jul 25, 2024

  1. testing analysis

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  2. comment pdf summary setup

    @adamcantor22
    adamcantor22 committed Jul 25, 2024
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  3. testing sequencing runs in analysis

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    adamcantor22 committed Jul 25, 2024
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  4. separate test users

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    adamcantor22 committed Jul 25, 2024
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  5. correct study name, wait for upload

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Commits on Aug 5, 2024

  1. reset permissions

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  2. try to get concurrently running watcher process to be recorded in cod… 

    …ecov
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  3. test revert

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  4. append to coverage

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  5. not for server tests

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Commits on Aug 6, 2024

  1. snakemake tests

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  2. test

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  3. remove snakemake logs

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    adamcantor22 committed Aug 6, 2024
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  4. gitignore

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    adamcantor22 committed Aug 6, 2024
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  5. add to pipeline

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    adamcantor22 committed Aug 6, 2024
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  6. install graphviz separately because it won't go into a /bin

    @adamcantor22
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  7. add append to coverage run command

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  8. try to get watcher to report its coverage

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  9. typo

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  10. specify coverage file locations

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    adamcantor22 committed Aug 6, 2024
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  11. run watcher as a subprocess on github actions

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  12. dont make an infinite loop

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Commits on Aug 7, 2024

  1. get spawn to track

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  2. correct syntax

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  3. coveragerc path

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    adamcantor22 committed Aug 7, 2024
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  4. folder breakdown by var

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  5. Merge branch 'Enhancement-SnakemakeAnalysis' of https://github.com/cl… 

    …emente-lab/mmeds-meta into Enhancement-SnakemakeAnalysis
    @adamcantor22
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  6. correct paths

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  7. test files

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  8. pathing

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  9. NAs in filenames

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  10. pathing in DAA

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    adamcantor22 committed Aug 7, 2024
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  11. remove tool class

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  12. dont test something that doesnt exist

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  13. cleanup

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  14. job template

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Commits on Aug 8, 2024

  1. moving tool tests to analysis tests

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  2. moving files

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  3. fix object control

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    adamcantor22 committed Aug 8, 2024
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  4. update workflow

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  5. pip not apt

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  6. adding lefse tests

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  7. deprecating summaries for now

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  8. cleaning up development stuff

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  9. changing pipeline name

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  10. changing pipeline name

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Commits on Aug 14, 2024

  1. generalizing filter to two classes for both lefse and ancombc

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  2. diversity output as directory

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    adamcantor22 committed Aug 14, 2024
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  3. dashes for table filtering

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  4. limit ancombc filterings

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  5. handle ancombc edge case with two classes + nan, also make filtered t… 

    …ables more manageable
    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  6. fix building phylo tree

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  7. typos

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  8. fix table extraction ambiguity

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  9. typo

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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  10. give more complex process more memory

    @adamcantor22
    adamcantor22 committed Aug 14, 2024
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Commits on Aug 15, 2024

  1. fixing ancombc, did not need all those splits

    @adamcantor22
    adamcantor22 committed Aug 15, 2024
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  2. unneccesary resource management

    @adamcantor22
    adamcantor22 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. missing conda env spec

    @adamcantor22
    adamcantor22 committed Aug 16, 2024
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  2. give ancombc more memory

    @adamcantor22
    adamcantor22 committed Aug 16, 2024
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  3. remove previous

    @adamcantor22
    adamcantor22 committed Aug 16, 2024
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  4. verbose

    @adamcantor22
    adamcantor22 committed Aug 16, 2024
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Commits on Aug 30, 2024

  1. unique() fix and template updates

    @adamcantor22
    adamcantor22 committed Aug 30, 2024
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Commits on Sep 11, 2024

  1. dual barcodes updates

    @adamcantor22
    adamcantor22 committed Sep 11, 2024
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