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Reorganize to new targene-pipeline structure #5

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Reorganize to new targene-pipeline structure #5

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Commits on Oct 1, 2024

  1. add ukb_image

    @roskamsh
    roskamsh committed Oct 1, 2024
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  2. add new cluster options

    @roskamsh
    roskamsh committed Oct 1, 2024
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  3. update to recent targene code and rearrange subworkflows/modules

    @roskamsh
    roskamsh committed Oct 1, 2024
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  4. working test config with GenOMICC data

    @roskamsh
    roskamsh committed Oct 1, 2024
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  5. remove old extract module

    @roskamsh
    roskamsh committed Oct 1, 2024
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  6. move these modules to confounders.nf

    @roskamsh
    roskamsh committed Oct 1, 2024
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  7. add genotypes.nf processes into here

    @roskamsh
    roskamsh committed Oct 1, 2024
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  8. update to new targene version and rearrange subworkflows/modules

    @roskamsh
    roskamsh committed Oct 1, 2024
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  9. add missing containers & rename

    @roskamsh
    roskamsh committed Oct 1, 2024
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  10. change UKBB cohort name to UKB

    @roskamsh
    roskamsh committed Oct 1, 2024
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  11. update default UKB_CONFIG specification

    @roskamsh
    roskamsh committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. update to most recent resource specifications

    @roskamsh
    roskamsh committed Oct 2, 2024
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  2. add exit status 135 & revert back to old clusterOptions

    @roskamsh
    roskamsh committed Oct 2, 2024
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  3. fix bug where task couldn't re-submit on retries

    @roskamsh
    roskamsh committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. add old cluster options back in

    @roskamsh
    roskamsh committed Oct 3, 2024
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  2. add run_type default

    @roskamsh
    roskamsh committed Oct 3, 2024
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  3. update CHR_FORMAT for ld block removal range

    @roskamsh
    roskamsh committed Oct 3, 2024
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  4. fix file configuration

    @roskamsh
    roskamsh committed Oct 3, 2024
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  5. update SNPs to match targene-pipeline

    @roskamsh
    roskamsh committed Oct 3, 2024
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  6. add RUN_TYPE

    @roskamsh
    roskamsh committed Oct 3, 2024
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  7. add new profiles

    @roskamsh
    roskamsh committed Oct 3, 2024
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  8. add first try CI yaml

    @roskamsh
    roskamsh committed Oct 3, 2024
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  9. add CI config

    @roskamsh
    roskamsh committed Oct 3, 2024
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  10. add docker config

    @roskamsh
    roskamsh committed Oct 3, 2024
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  11. add local config

    @roskamsh
    roskamsh committed Oct 3, 2024
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  12. python requirements for tests

    @roskamsh
    roskamsh committed Oct 3, 2024
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  13. first end-to-end test script

    @roskamsh
    roskamsh committed Oct 3, 2024
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  14. update path

    @roskamsh
    roskamsh committed Oct 3, 2024
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  15. update command-line argument to pytest

    @roskamsh
    roskamsh committed Oct 3, 2024
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  16. add pytest

    @roskamsh
    roskamsh committed Oct 3, 2024
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  17. add additional teste using pytest

    @roskamsh
    roskamsh committed Oct 3, 2024
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  18. move command declaration into function

    @roskamsh
    roskamsh committed Oct 3, 2024
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  19. update tests

    @roskamsh
    roskamsh committed Oct 3, 2024
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