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[TheiaCoV] Split database from Kraken2_TheiaCoV task #670

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[TheiaCoV] Split database from Kraken2_TheiaCoV task #670

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Commits on Nov 7, 2024

  1. kraken2_theiacov: Split db from container, update both; minor improve… 

    …ments on krakren2 command call; improvememnts on target organism parse to report proportion of sc2 only if target org is sc2
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    cimendes committed Nov 7, 2024
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  2. set tartget org as sc2, can be user modified

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    cimendes committed Nov 7, 2024
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  3. Floar sc2 percent -> string sc2 percent to allow empty values

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    cimendes committed Nov 7, 2024
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  4. passing on target org to output percent of sc2

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    cimendes committed Nov 7, 2024
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  5. add kraken target org to sc2, update target org of rsv-a and rsv-b

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    cimendes committed Nov 7, 2024
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  6. percent sc2 from float to string to allow empty values

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    cimendes committed Nov 7, 2024
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  7. clarify input name

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    cimendes committed Nov 7, 2024
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  8. add test DB for theiacov kraken2; update CI inputs for TheiaCoV clear… 

    …labs
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    cimendes committed Nov 7, 2024
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  9. ops, must be File not String

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    cimendes committed Nov 7, 2024
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  10. expose kraken2_theiacov database and runtime parameters

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    cimendes committed Nov 7, 2024
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  11. expose runtime parameters and db for theiacov's kraken2

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    cimendes committed Nov 7, 2024
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  12. update inputs

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    cimendes committed Nov 7, 2024
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  13. update CI for theiacov_clearlabs

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    cimendes committed Nov 7, 2024
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  14. update md5sums

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    cimendes committed Nov 7, 2024
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  15. do the same for theiacov_ont

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    cimendes committed Nov 7, 2024
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  16. fix bug

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    cimendes committed Nov 7, 2024
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  17. update CI

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    cimendes committed Nov 7, 2024
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  18. update CI

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    cimendes committed Nov 7, 2024
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  19. update docs - freyja

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    cimendes committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. update docs - theiacov

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    cimendes committed Nov 8, 2024
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