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New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #1388

Merged
merged 38 commits into from
Sep 19, 2024
Merged

New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #1388

merged 38 commits into from
Sep 19, 2024

Commits on Jul 30, 2024

  1. Install kraken2 and bracken

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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  2. Change nextflow configurations

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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  3. Initial addition of kraken and bracken to pipeline

    @egreenberg7
    egreenberg7 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Fix include statements

    @egreenberg7
    egreenberg7 committed Jul 31, 2024
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  2. Fix include statements

    @egreenberg7
    egreenberg7 committed Jul 31, 2024
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Commits on Aug 5, 2024

  1. Include module config files

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  2. Use presence of kraken_db to determine bracken run, add save params

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  3. Fix multiqc for Bracken/Kraken

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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  4. Add Bracken/Kraken citations

    @egreenberg7
    egreenberg7 committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Fix bracken config

    @egreenberg7
    egreenberg7 committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Update bracken

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  2. Adjust multiqc configs for updated bracken

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  3. Add input validation and update scheme

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  4. Change default Bracken precision to species

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  5. Debug input validation

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  6. Documentation/output image

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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  7. Update changelog

    @egreenberg7
    egreenberg7 committed Aug 7, 2024
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Commits on Aug 9, 2024

  1. Update Kraken2 module

    @egreenberg7
    egreenberg7 committed Aug 9, 2024
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  2. Linting

    @egreenberg7
    egreenberg7 committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. Change to --contaminant_screening param

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  2. Fixing save unaligned default

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  3. Debugging

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  4. Update usage

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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  5. Provide motivation for Kraken2 parameters

    @egreenberg7
    egreenberg7 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Fix typo

    @egreenberg7
    egreenberg7 committed Aug 16, 2024
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  2. Update metro map

    @egreenberg7
    egreenberg7 committed Aug 16, 2024
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Commits on Aug 18, 2024

  1. Merge branch 'dev' into dev

    @Shaun-Regenbaum
    Shaun-Regenbaum authored Aug 18, 2024
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Commits on Aug 19, 2024

  1. Update schema

    @egreenberg7
    egreenberg7 committed Aug 19, 2024
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  2. Update docs/usage.md 

    Co-authored-by: Matthias Zepper <[email protected]>
    @egreenberg7 @MatthiasZepper
    egreenberg7 and MatthiasZepper authored Aug 19, 2024
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  3. Change output directory for kraken2/bracken

    @egreenberg7
    egreenberg7 committed Aug 19, 2024
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Commits on Sep 10, 2024

  1. Update Changelog

    @egreenberg7
    egreenberg7 committed Sep 10, 2024
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  2. Another changelog fix

    @egreenberg7
    egreenberg7 committed Sep 10, 2024
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  3. Linting fix

    @egreenberg7
    egreenberg7 committed Sep 10, 2024
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Commits on Sep 19, 2024

  1. Merge conflcits

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  2. Merge branch 'dev' of github.com:egreenberg7/rnaseq into dev

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  3. Update hisat2 patch

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  4. (Hopefully) final linting fix

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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  5. Change PR number

    @egreenberg7
    egreenberg7 committed Sep 19, 2024
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