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Anndata #92

Merged
merged 41 commits into from
Apr 8, 2024
Merged

Anndata #92

merged 41 commits into from
Apr 8, 2024

Commits on Aug 10, 2023

  1. Moved cags out of alignment, without testing yet for OK

    Jonathan Golob committed Aug 10, 2023
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  2. Brought back alignment workflow outputs for now

    Jonathan Golob committed Aug 10, 2023
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  3. renamed alignment to quantify to better reflect objective not approach

    Jonathan Golob committed Aug 10, 2023
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  4. Basic working anndata format of the abundance output.

    Jonathan Golob committed Aug 10, 2023
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  5. Allow for custom prefix of output

    Jonathan Golob committed Aug 10, 2023
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Commits on Oct 6, 2023

  1. ignore rather than finish

    Jonathan Golob committed Oct 6, 2023
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Commits on Oct 20, 2023

  1. Add annotation models invocation

    Jonathan Golob committed Oct 20, 2023
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  2. Added main

    Jonathan Golob committed Oct 20, 2023
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Commits on Oct 30, 2023

  1. Update eggnog-mapper version

    @sminot
    sminot committed Oct 30, 2023
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  2. Document database setup

    @sminot
    sminot committed Oct 30, 2023
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  3. Clean up functional annotation workflow

    @sminot
    sminot committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. Starting to rework tests to fit new structure and outputs

    Jonathan Golob committed Nov 1, 2023
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  2. Test for preprocesing module.

    Jonathan Golob committed Nov 1, 2023
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  3. Simplified barcodecop

    Jonathan Golob committed Nov 1, 2023
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  4. New barcodecop image

    Jonathan Golob committed Nov 1, 2023
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  5. Removed extraneous )

    Jonathan Golob committed Nov 1, 2023
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  6. Human -> Host.

    Jonathan Golob committed Nov 1, 2023
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  7. Cleaned up mock manifest and flow through

    Jonathan Golob committed Nov 1, 2023
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  8. a bit more fake data

    Jonathan Golob committed Nov 1, 2023
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  9. preprocressing plus tests updated

    Jonathan Golob committed Nov 1, 2023
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  10. Only one correct validate output

    Jonathan Golob committed Nov 1, 2023
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  11. Cleaned up names of test

    Jonathan Golob committed Nov 1, 2023
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  12. New example outputs

    Jonathan Golob committed Nov 1, 2023
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  13. Corrected tests and example output

    Jonathan Golob committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. Removed old example output and have modified composition

    Jonathan Golob committed Nov 2, 2023
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  2. Tests for composition and example output.

    Jonathan Golob committed Nov 2, 2023
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  3. Allele catalog with contigs broken out

    Jonathan Golob committed Nov 2, 2023
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  4. Add tests for contig and allele catalog

    Jonathan Golob committed Nov 2, 2023
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  5. Clustering module

    Jonathan Golob committed Nov 2, 2023
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  6. Corrected test typo

    Jonathan Golob committed Nov 2, 2023
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  7. Corrected tests

    Jonathan Golob committed Nov 2, 2023
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  8. quantify module...

    Jonathan Golob committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. Added example quantity outputs

    Jonathan Golob committed Nov 3, 2023
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  2. Corrected tests to use config and profile

    Jonathan Golob committed Nov 3, 2023
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  3. Removed duplicative diamond index process

    Jonathan Golob committed Nov 3, 2023
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  4. Merge pull request #90 from Golob-Minot/anndata_eggnog 

    Update annotation workflow
    @jgolob
    jgolob committed Nov 3, 2023
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  5. Corrected diamond makedb 

    Added more details to annotation database downloading.
    Jonathan Golob committed Nov 3, 2023
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  6. Merge branch 'anndata' of ssh://github.com/Golob-Minot/geneshot into … 

    …anndata
    Jonathan Golob committed Nov 3, 2023
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  7. Make output conform to remainder of modules

    Jonathan Golob committed Nov 3, 2023
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Commits on Apr 8, 2024

  1. Much tighter query ID and coverage defaults fitting the intent to ali… 

    …gn back to the same reference..
    Jonathan Golob committed Apr 8, 2024
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  2. Added in a proper merge of fastq and corrected qc manifest

    Jonathan Golob committed Apr 8, 2024
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