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chore: improvements to generate 2401 data release #436

Merged
merged 25 commits into from
Jan 18, 2024
Merged

chore: improvements to generate 2401 data release #436

merged 25 commits into from
Jan 18, 2024

Commits on Jan 17, 2024

  1. fix(dag): remove ot_gwas_catalog ot_study_locus_overlap from etl dag … 

    …steps
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    ireneisdoomed committed Jan 17, 2024
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  2. fix(dag): remove ot_gwas_catalog ot_study_locus_overlap from etl dag … 

    …steps
    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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  3. fix: include gene_index as a release output

    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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  4. feat(l2g): split step into train and predict

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    ireneisdoomed committed Jan 17, 2024
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  5. chore(dag): add colocalisation step

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  6. feat(l2g): split step into train and predict

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  7. chore: rename ot_v2g config to unabbreviated name

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    ireneisdoomed committed Jan 17, 2024
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  8. chore(colocalisation): remove coloc parameters from config

    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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  9. fix(colocalisation): update credible set path in config

    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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  10. fix(l2g): remove overlaps from config

    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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  11. chore(dag): remove ukbiobank and eqtl from preprocess

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  12. fix(l2g): increase driver and executors memory

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    ireneisdoomed committed Jan 17, 2024
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  13. fix(l2g): make training dependencies optional

    @ireneisdoomed
    ireneisdoomed committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. fix(l2g): drop studyType before creating gwas_study_locus

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  2. fix(l2g): convert features_list from config to list

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  3. fix(l2g): include mean vep features in feature_list

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  4. chore: change default driver node to n1-highmem-16

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  5. revert(l2g): revert 4eafaf2

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  6. Merge branch 'dev' of https://github.com/opentargets/genetics_etl_python 

     into il-generate-2401
    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  7. chore: fetch etl inputs from new data structure

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  8. feat(study_locus): add and test filter_by_study_type

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  9. feat(study_locus): add and test filter_by_study_type

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  10. feat(l2g): limit l2g predictions to gwas-derived associations

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  11. fix: typo in test_filter_by_study_type

    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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  12. Merge branch 'dev' of https://github.com/opentargets/genetics_etl_python 

     into il-generate-2401
    @ireneisdoomed
    ireneisdoomed committed Jan 18, 2024
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