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Drop aggregation during report generation #249

Merged
merged 48 commits into from
Feb 29, 2024
Merged

Drop aggregation during report generation #249

merged 48 commits into from
Feb 29, 2024

Commits on Feb 21, 2024

  1. drop small sampleset warning when integrating reference data

    @nebfield
    nebfield committed Feb 21, 2024
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  2. drop aggregation

    @nebfield
    nebfield committed Feb 21, 2024
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  3. update lockfile: drop data.table

    @nebfield
    nebfield committed Feb 21, 2024
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  4. load scores the same way

    @nebfield
    nebfield committed Feb 21, 2024
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  5. bump utils version

    @nebfield
    nebfield committed Feb 21, 2024
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  6. drop effect_type (shouldn't actually be in columns array)

    @nebfield
    nebfield committed Feb 21, 2024
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Commits on Feb 22, 2024

  1. use dev image

    @nebfield
    nebfield committed Feb 22, 2024
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  2. update score test

    @nebfield
    nebfield committed Feb 22, 2024
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  3. fix test

    @nebfield
    nebfield committed Feb 22, 2024
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  4. bump pgscatalog_utils version

    @nebfield
    nebfield committed Feb 22, 2024
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  5. boring but big: re-sync nf-core

    @nebfield
    nebfield committed Feb 22, 2024
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  6. fix cache error in report

    @nebfield
    nebfield committed Feb 22, 2024
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  7. nf-core resync

    @nebfield
    nebfield committed Feb 22, 2024
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  8. set deno dir

    @nebfield
    nebfield committed Feb 22, 2024
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  9. update schema

    @nebfield
    nebfield committed Feb 22, 2024
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  10. set up auto-generated environment

    @nebfield
    nebfield committed Feb 22, 2024
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  11. set workDir consistently

    @nebfield
    nebfield committed Feb 22, 2024
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  12. improve caching

    @nebfield
    nebfield committed Feb 22, 2024
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  13. fix help

    @nebfield
    nebfield committed Feb 22, 2024
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  14. set outdir default

    @nebfield
    nebfield committed Feb 22, 2024
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  15. Merge pull request #250 from PGScatalog/resyncnf 

    re-sync nf-core
    @nebfield
    nebfield authored Feb 22, 2024
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  16. use binary packages to build report image

    @nebfield
    nebfield committed Feb 22, 2024
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  17. fix missing dependencies

    @nebfield
    nebfield committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. fix fraposa_pca

    @nebfield
    nebfield committed Feb 23, 2024
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  2. add storeDir to relabel_ids

    @nebfield
    nebfield committed Feb 23, 2024
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  3. fix score metadata in report

    @nebfield
    nebfield committed Feb 23, 2024
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  4. store results permanently

    @nebfield
    nebfield committed Feb 23, 2024
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  5. write to genotypes_cache, if set

    @nebfield
    nebfield committed Feb 23, 2024
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  6. update conda

    @nebfield
    nebfield committed Feb 23, 2024
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  7. add custom example scorefile

    @nebfield
    nebfield committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Update schema to say what the cache is for

    @smlmbrt
    smlmbrt committed Feb 26, 2024
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  2. Add information on cache and pipeline speed

    @smlmbrt
    smlmbrt committed Feb 26, 2024
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  3. Not only for -resume

    @smlmbrt
    smlmbrt committed Feb 26, 2024
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  4. fix storeDir

    @nebfield
    nebfield committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. fix tempdir on HPC/singularity

    @nebfield
    nebfield committed Feb 27, 2024
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  2. gcp compatbility updates

    @nebfield
    nebfield committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. remove semantic structure from storeDirs (bad)

    @nebfield
    nebfield committed Feb 28, 2024
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  2. Merge branch 'drop-report-aggregation' into fix-cloud

    @nebfield
    nebfield authored Feb 28, 2024
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  3. Update cache.rst

    @smlmbrt
    smlmbrt authored Feb 28, 2024
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  4. Merge branch 'drop-report-aggregation' into docs_cache

    @nebfield
    nebfield authored Feb 28, 2024
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  5. Merge pull request #254 from PGScatalog/docs_cache 

    Docs to explain cache
    @nebfield
    nebfield authored Feb 28, 2024
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  6. Merge pull request #256 from PGScatalog/fix-cloud 

    Remove storeDir semantic structure
    @nebfield
    nebfield authored Feb 28, 2024
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  7. don't copy twice

    @nebfield
    nebfield committed Feb 28, 2024
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  8. bump report singularity version

    @nebfield
    nebfield committed Feb 28, 2024
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  9. fix quarto

    @nebfield
    nebfield committed Feb 28, 2024
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Commits on Feb 29, 2024

  1. fix output

    @nebfield
    nebfield committed Feb 29, 2024
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  2. fix fraposa

    @nebfield
    nebfield committed Feb 29, 2024
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  3. fix capturing intersect counts

    @nebfield
    nebfield committed Feb 29, 2024
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