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Add kraken2 phylogenetic assignment subworkflow #47

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Add kraken2 phylogenetic assignment subworkflow #47

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Commits on Oct 28, 2024

  1. first commit with kraken2 module

    @ctuni
    ctuni committed Oct 28, 2024
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  2. added a database to the config

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    ctuni committed Oct 28, 2024
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  3. added kraken2 param to schema

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    ctuni committed Oct 28, 2024
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  4. readded modules

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  5. fixed kraken2 name

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    ctuni committed Oct 28, 2024
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  6. added missing kraken2 options

    @ctuni
    ctuni committed Oct 28, 2024
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  7. fixed something in the linting

    @ctuni
    ctuni committed Oct 28, 2024
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  8. added output to multiqc

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  9. changed the kraken2 channels

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  10. removed kraken2 from mutiqc for now

    @ctuni
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  11. added kraken2 reports to the multqc channel

    @ctuni
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  12. trying other methods to creae the multiqc files channel

    @ctuni
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  13. trying to pass kraken2 report to multiqc

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  14. why is multiqc not working?

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  15. why is multiqc not working?

    @ctuni
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  16. ugh

    @ctuni
    ctuni committed Oct 28, 2024
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  17. removed kraken2 from multiqc files

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  18. updated schema

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  19. Merge branch 'dev' into feature/kraken2

    @ctuni
    ctuni authored Oct 28, 2024
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  20. fixing some things

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  21. changed schema version

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  22. trying to unbreak things

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  23. added prettier

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  24. further unbreaking things

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  25. re-updated schema

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  26. prettier

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  27. forgot to change changelog

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    ctuni committed Oct 28, 2024
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  28. added krona plots to the emit block and added check for uncompressed … 

    …kraken2 db
    @ctuni
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Commits on Oct 29, 2024

  1. fixed typo

    @ctuni
    ctuni committed Oct 29, 2024
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  2. several improvements

    @ctuni
    ctuni committed Oct 29, 2024
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  3. prettier

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  4. updated citations

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  5. Update docs/output.md 

    Co-authored-by: Natalia Garcia Garcia <[email protected]>
    @ctuni @nggvs
    ctuni and nggvs authored Oct 29, 2024
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  6. updated output

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  7. updated output

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Commits on Oct 30, 2024

  1. Merge branch 'dev' into feature/kraken2

    @ctuni
    ctuni authored Oct 30, 2024
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  2. added kraken2 reports to multiqc

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    ctuni committed Oct 30, 2024
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  3. Merge branch 'feature/kraken2' of https://github.com/ctuni/seqinspector… 

    … into feature/kraken2
    @ctuni
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  4. schema

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  5. Merge branch 'dev' into feature/kraken2

    @ctuni
    ctuni authored Oct 30, 2024
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  6. Merge branch 'feature/kraken2' of https://github.com/ctuni/seqinspector… 

    … into feature/kraken2
    @ctuni
    ctuni committed Oct 30, 2024
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  7. prettier

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    ctuni committed Oct 30, 2024
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  8. Update workflows/seqinspector.nf 

    Removed debugging commented statement

Co-authored-by: Natalia Garcia Garcia <[email protected]>
    @ctuni @nggvs
    ctuni and nggvs authored Oct 30, 2024
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  9. disabled the publish of the taxonomy file

    @ctuni
    ctuni committed Oct 30, 2024
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  10. Merge branch 'feature/kraken2' of https://github.com/ctuni/seqinspector… 

    … into feature/kraken2
    @ctuni
    ctuni committed Oct 30, 2024
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  11. removed default database for a null one

    @ctuni
    ctuni committed Oct 30, 2024
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  12. added test kraken2 database to the test configs

    @ctuni
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  13. fixed typo

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    ctuni committed Oct 30, 2024
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  14. miseq test is failing

    @ctuni
    ctuni committed Oct 30, 2024
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  15. miseq test is failing

    @ctuni
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  16. promethion test is failing

    @ctuni
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  17. novaseq test is failing

    @ctuni
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  18. novaseq test is failing

    @ctuni
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