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v2.0.0-beta.2 #341

Merged
merged 37 commits into from
Jul 31, 2024
Merged

v2.0.0-beta.2 #341

merged 37 commits into from
Jul 31, 2024

Commits on Jul 10, 2024

  1. Remove references to multiple cohorts

    @nebfield
    nebfield authored Jul 10, 2024
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Commits on Jul 15, 2024

  1. Update container tags to use ghcr

    @nebfield
    nebfield authored Jul 15, 2024
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Commits on Jul 19, 2024

  1. read bim files with --stu_filt_iid

    @nebfield
    nebfield committed Jul 19, 2024
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  2. write fid in plink2 --score

    @nebfield
    nebfield committed Jul 19, 2024
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  3. split the fam output, not the psam

    @nebfield
    nebfield committed Jul 19, 2024
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  4. fix report support for FID

    @nebfield
    nebfield committed Jul 19, 2024
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  5. Merge branch 'main' into dev

    @nebfield
    nebfield authored Jul 19, 2024
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  6. fix line ending

    @nebfield
    nebfield committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. bump fraposa version

    @nebfield
    nebfield committed Jul 22, 2024
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Commits on Jul 24, 2024

  1. remove duplicated changelog

    @nebfield
    nebfield committed Jul 24, 2024
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Commits on Jul 29, 2024

  1. remove duplicated changelog

    @nebfield
    nebfield committed Jul 29, 2024
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  2. bump pgscatalog-utils version

    @nebfield
    nebfield committed Jul 29, 2024
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  3. Merge branch 'dev' into docs-review

    @nebfield
    nebfield authored Jul 29, 2024
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  4. update schema with support for --maf_target and --geno_miss_target

    @nebfield
    nebfield committed Jul 29, 2024
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  5. update directory path

    @nebfield
    nebfield committed Jul 29, 2024
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  6. Fix and add schema descriptions.

    @smlmbrt
    smlmbrt committed Jul 29, 2024
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  7. Clarifying changes to PCA variant parameters.

    @smlmbrt
    smlmbrt committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. remove default anaconda channels (#342) 

    * remove default anaconda channels

* use nodefaults in all conda environment files
    @nebfield
    nebfield authored Jul 30, 2024
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  2. fix group name (matching options)

    @nebfield
    nebfield committed Jul 30, 2024
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  3. update schema with support for --maf_target and --geno_miss_target

    @nebfield
    nebfield committed Jul 30, 2024
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  4. bump version

    @nebfield
    nebfield committed Jul 30, 2024
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  5. docs review

    @nebfield
    nebfield committed Jul 30, 2024
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  6. Merge branch 'dev' into docs-review

    @nebfield
    nebfield authored Jul 30, 2024
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  7. Documenting new target MAF/missingness variant filters in explainer.

    @smlmbrt
    smlmbrt committed Jul 30, 2024
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  8. remove biocontainers from citations

    @nebfield
    nebfield authored Jul 30, 2024
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  9. update link from pgscatalog_utils to pygscatalog

    @nebfield
    nebfield authored Jul 30, 2024
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  10. Re-align param names and module with schema

    @smlmbrt
    smlmbrt committed Jul 30, 2024
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  11. Add to conf

    @smlmbrt
    smlmbrt committed Jul 30, 2024
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  12. Merge pull request #336 from PGScatalog/docs-review 

    Review docs
    @smlmbrt
    smlmbrt authored Jul 30, 2024
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Commits on Jul 31, 2024

  1. Update gitignore

    @nebfield
    nebfield committed Jul 31, 2024
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  2. Don't filter TARGET variants for MAF by default, the missingness filt… 

    …er remains the same.
    @smlmbrt
    smlmbrt committed Jul 31, 2024
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  3. add --efo_id parameter

    @nebfield
    nebfield committed Jul 31, 2024
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  4. update trait_efo -> efo_id

    @nebfield
    nebfield committed Jul 31, 2024
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  5. check if --efo_id is set when workflow starts

    @nebfield
    nebfield committed Jul 31, 2024
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  6. Typo fix

    @smlmbrt
    smlmbrt authored Jul 31, 2024
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  7. Merge branch 'dev' into pca_maf_0

    @smlmbrt
    smlmbrt authored Jul 31, 2024
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  8. Merge pull request #344 from PGScatalog/pca_maf_0 

    Don't filter TARGET variants for MAF by default, the missingness filt…
    @nebfield
    nebfield authored Jul 31, 2024
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