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Allofus - Adapt targene for use on the All of Us Researcher Workbench #174

Merged
merged 100 commits into from
Nov 13, 2024
Merged

Allofus - Adapt targene for use on the All of Us Researcher Workbench #174

merged 100 commits into from
Nov 13, 2024

Commits on May 10, 2024

  1. add all of us profile

    @roskamsh
    roskamsh committed May 10, 2024
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  2. add test config file to test running targene on AOU RW

    @roskamsh
    roskamsh committed May 10, 2024
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  3. add all of us profile configuration

    @roskamsh
    roskamsh committed May 10, 2024
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  4. add actual test input data example

    @roskamsh
    roskamsh committed May 10, 2024
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  5. rearrange some baseline settings into the profile for allofus

    @roskamsh
    roskamsh committed May 10, 2024
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  6. rearrange some parameters

    @roskamsh
    roskamsh committed May 10, 2024
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Commits on Sep 12, 2024

  1. add allofus profile currently working

    @roskamsh
    roskamsh committed Sep 12, 2024
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  2. remove olf file

    @roskamsh
    roskamsh committed Sep 12, 2024
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  3. add working container declaration in AOU RW

    @roskamsh
    roskamsh committed Sep 12, 2024
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  4. working test configuration for all of us

    @roskamsh
    roskamsh committed Sep 12, 2024
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Commits on Sep 16, 2024

  1. remove old file

    @roskamsh
    roskamsh committed Sep 16, 2024
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  2. Merge branch 'main' into allofus

    @roskamsh
    roskamsh committed Sep 16, 2024
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Commits on Sep 18, 2024

  1. update input parameters to be consistent with new version

    @roskamsh
    roskamsh committed Sep 18, 2024
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  2. add gls and allofus profiles

    @roskamsh
    roskamsh committed Sep 18, 2024
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  3. update flashpca and add baseline commandlinetools container

    @roskamsh
    roskamsh committed Sep 18, 2024
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  4. remove gls config

    @roskamsh
    roskamsh committed Sep 18, 2024
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  5. add all of us RW specifications to run with gls profile included in ~… 

    …/.nextflow/config
    @roskamsh
    roskamsh committed Sep 18, 2024
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  6. add dockerfile for flashPCA container

    Breeshey Roskams-Hieter committed Sep 18, 2024
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  7. update to flashpca container version

    Breeshey Roskams-Hieter committed Sep 18, 2024
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Commits on Sep 24, 2024

  1. address Olivier's comment; reorganize container declaration

    @roskamsh
    roskamsh committed Sep 24, 2024
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  2. missing quotation

    @roskamsh
    roskamsh committed Sep 24, 2024
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  3. base image only required when running only through docker on aou rw

    @roskamsh
    roskamsh committed Sep 24, 2024
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  4. retain image naming system

    @roskamsh
    roskamsh committed Sep 24, 2024
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Commits on Oct 24, 2024

  1. Merge branch 'main' into allofus

    @roskamsh
    roskamsh committed Oct 24, 2024
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  2. Revert "retain image naming system" 

    This reverts commit e5fb4f5.
    @roskamsh
    roskamsh committed Oct 24, 2024
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  3. Revert "Revert "retain image naming system"" 

    This reverts commit f0edfea.
    @roskamsh
    roskamsh committed Oct 24, 2024
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  4. fix syntax

    @roskamsh
    roskamsh committed Oct 24, 2024
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  5. fix julia version to matcg Manifest

    @roskamsh
    roskamsh committed Oct 24, 2024
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Commits on Nov 2, 2024

  1. add calculateCpus function for task memory in all of us profile

    @roskamsh
    roskamsh committed Nov 2, 2024
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  2. move to allofus.conf

    @roskamsh
    roskamsh committed Nov 2, 2024
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  3. add function to create empty ESTIMATORS_CONFIG file if doesn't exist

    @roskamsh
    roskamsh committed Nov 2, 2024
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  4. add processEstimatorsConfig() as input rather than reading directly f… 

    …rom params.ESTIMATORS_CONFIG
    @roskamsh
    roskamsh committed Nov 2, 2024
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  5. remove unnecessary test.config file

    @roskamsh
    roskamsh committed Nov 2, 2024
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  6. remove Dockerfile from this branch, now on dockerfiles branch

    @roskamsh
    roskamsh committed Nov 2, 2024
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  7. update function to handle list cases

    @roskamsh
    roskamsh committed Nov 2, 2024
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  8. pass params.ESTIMATORS_CONFIG in as an argument

    @roskamsh
    roskamsh committed Nov 2, 2024
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  9. fix instance where julia file is actually provided

    @roskamsh
    roskamsh committed Nov 2, 2024
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  10. update calculateCpus function to run without error on AOU RW

    @roskamsh
    roskamsh committed Nov 2, 2024
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Commits on Nov 5, 2024

  1. update .gitignore

    @roskamsh
    roskamsh committed Nov 5, 2024
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  2. add ESTIMANDS_CONFIG for no QQ run

    @roskamsh
    roskamsh committed Nov 5, 2024
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  3. provide subsetted traits file

    @roskamsh
    roskamsh committed Nov 5, 2024
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  4. write configuration for no QQ run

    @roskamsh
    roskamsh committed Nov 5, 2024
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  5. update targene core image to qqplot_bug branch

    @roskamsh
    roskamsh committed Nov 5, 2024
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  6. add optional output of QQ plot

    @roskamsh
    roskamsh committed Nov 5, 2024
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  7. update

    @roskamsh
    roskamsh committed Nov 5, 2024
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  8. add julia file for no QQ plot end-to-end test

    @roskamsh
    roskamsh committed Nov 5, 2024
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  9. Merge branch 'allofus' of github.com:TARGENE/targene-pipeline into al… 

    …lofus
    @roskamsh
    roskamsh committed Nov 5, 2024
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  10. add no QQ plot test

    @roskamsh
    roskamsh committed Nov 5, 2024
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  11. update test script to fit new targene run

    @roskamsh
    roskamsh committed Nov 5, 2024
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Commits on Nov 6, 2024

  1. remove no_qq test

    @roskamsh
    roskamsh committed Nov 6, 2024
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  2. remove no qq test files

    @roskamsh
    roskamsh committed Nov 6, 2024
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  3. add test

    @roskamsh
    roskamsh committed Nov 6, 2024
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  4. add empty QQ test

    @roskamsh
    roskamsh committed Nov 6, 2024
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  5. make QQ plot non-optional

    @roskamsh
    roskamsh committed Nov 6, 2024
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  6. add example run with the All of Us cohort

    @roskamsh
    roskamsh committed Nov 6, 2024
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  7. add new allofus doc

    @roskamsh
    roskamsh committed Nov 6, 2024
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  8. add All of Us cohort section

    @roskamsh
    roskamsh committed Nov 6, 2024
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  9. up targene version

    @roskamsh
    roskamsh committed Nov 6, 2024
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  10. update formatting

    @roskamsh
    roskamsh committed Nov 6, 2024
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  11. update test now that QQ is created even for single p-value runs

    @roskamsh
    roskamsh committed Nov 6, 2024
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Commits on Nov 7, 2024

  1. update process EstimatorsConfig to handle lists appropriately

    @roskamsh
    roskamsh committed Nov 7, 2024
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  2. update test name

    @roskamsh
    roskamsh committed Nov 7, 2024
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  3. address Olivier's comments

    @roskamsh
    roskamsh committed Nov 7, 2024
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  4. simplify run

    @roskamsh
    roskamsh committed Nov 7, 2024
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  5. handle list configurations appropriately and output Channel

    @roskamsh
    roskamsh committed Nov 7, 2024
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  6. add an additional estimator to test list case

    @roskamsh
    roskamsh committed Nov 7, 2024
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  7. update function call

    @roskamsh
    roskamsh committed Nov 7, 2024
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  8. update function call

    @roskamsh
    roskamsh committed Nov 7, 2024
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  9. update estimators config function call

    @roskamsh
    roskamsh committed Nov 7, 2024
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  10. de-couple file creation from channel creation

    @roskamsh
    roskamsh committed Nov 7, 2024
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  11. test new functions

    @roskamsh
    roskamsh committed Nov 7, 2024
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  12. test whether OUTDIR makes the difference

    @roskamsh
    roskamsh committed Nov 7, 2024
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  13. create OUTDIR if not already present

    @roskamsh
    roskamsh committed Nov 7, 2024
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  14. update estimators call

    @roskamsh
    roskamsh committed Nov 7, 2024
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  15. update null simulation to account for additional estimator

    @roskamsh
    roskamsh committed Nov 7, 2024
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  16. update realistic simulation to account for additional estimator

    @roskamsh
    roskamsh committed Nov 7, 2024
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  17. change input strucure to accomodate new estimators_config channel str… 

    …ucture
    @roskamsh
    roskamsh committed Nov 7, 2024
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  18. add new line

    @roskamsh
    roskamsh committed Nov 7, 2024
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  19. combine estimators channel with TMLE inputs

    @roskamsh
    roskamsh committed Nov 7, 2024
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  20. update targene core version

    @roskamsh
    roskamsh committed Nov 7, 2024
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  21. address Olivier's comments

    @roskamsh
    roskamsh committed Nov 7, 2024
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  22. address Olivier's comments

    @roskamsh
    roskamsh committed Nov 7, 2024
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  23. up targene version to v0.12.0 in docs

    @roskamsh
    roskamsh committed Nov 7, 2024
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  24. slightly longer resume time in new version, but all other tests pass

    @roskamsh
    roskamsh committed Nov 7, 2024
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  25. update new input for EstimationWorkflow

    @roskamsh
    roskamsh committed Nov 7, 2024
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  26. revert resume time back to 100

    @roskamsh
    roskamsh committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. try debugging with tmate on realistic simulations workflow

    @roskamsh
    roskamsh committed Nov 8, 2024
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  2. change targene version to v0.11.1 in docs

    @roskamsh
    roskamsh committed Nov 8, 2024
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  3. revert back to original test runs

    @roskamsh
    roskamsh committed Nov 8, 2024
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  4. revert to original test case

    @roskamsh
    roskamsh committed Nov 8, 2024
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  5. return to single-estimator tests

    @roskamsh
    roskamsh committed Nov 8, 2024
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  6. return to single-estimator tests

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    roskamsh committed Nov 8, 2024
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  7. update inputs to EstimationWorkflow

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    roskamsh committed Nov 8, 2024
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  8. correct targene version

    @roskamsh
    roskamsh committed Nov 8, 2024
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  9. up resume time to 200

    @roskamsh
    roskamsh committed Nov 8, 2024
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  10. remove unused functions

    @roskamsh
    roskamsh committed Nov 8, 2024
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  11. update error message, previous one results in compilation error

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    roskamsh committed Nov 8, 2024
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Commits on Nov 12, 2024

  1. put resume time back to 100

    @roskamsh
    roskamsh committed Nov 12, 2024
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  2. Merge branch 'allofus' of github.com:TARGENE/targene-pipeline into al… 

    …lofus
    @roskamsh
    roskamsh committed Nov 12, 2024
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Commits on Nov 13, 2024

  1. ensure file isn't recreated on resume

    @roskamsh
    roskamsh committed Nov 13, 2024
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