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Dev (#952)
* add task to write relatedness check to tsv (#930) * add task to write relatedness check to tsv * fix requirements * relatedness_check_table_path * add relatedness check file path to metadata.json * Benb/use metadata as source of family table load (#936) * use run metadata as source of family table load * ruff * Support gcs dirs in rsync (#932) * Support gcs dirs in rsync * ws * Gencode refactor to remove gcs (#934) * Gencode refactor to remove gcs * Fix * additional semi join (#947) * metadata parameters refactor (#946) * metadata parameters refactor * fix missing param * tweak * missed one * last one * fix test * last few bugfixes * fix * bump * missed one * change parameter type due to confusing bug * push * enum * Parse clinvar version from header (#949) * Parse clinvar version from header * responses activate * fix test * Dependency reordering so that `ValidateCallsetTask` runs before updating the reference data. (#950) * Parse clinvar version from header * Dependency reordering for reference data updates and validation * ruff * missed one * Revert relatedness changes * push * Fix import issue * Fix sample type * ruff * Fix import mocking * imports * responses activate * fix test * Tweaks * comment * Benb/check parsed clinvar version in complete (#951) * Parse clinvar version from header * First pass * Bump hail tables to https * correct dataset/dataset types * Fix clinvar mito * Fix combined * Dependency reordering for reference data updates and validation * ruff * missed one * Revert relatedness changes * push * Fix import issue * Fix sample type * ruff * Fix import mocking * imports * Missed one * First mocking pass * Finish mocks in reference data * responses activate * ruff * commas * fix test * Update compare_globals.py * import --------- Co-authored-by: Julia Klugherz <juliaklugherz@gmail.com>
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‎pyproject.toml

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@@ -29,7 +29,6 @@ extend-exclude = [
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'luigi_pipeline/lib/*',
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'luigi_pipeline/seqr*.py',
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'luigi_pipeline/tests/data/*',
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'v03_pipeline/lib/reference_data/gencode/*',
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]
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ignore = [
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# Individual Rules

‎requirements.in

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@@ -3,6 +3,5 @@ google-api-python-client>=1.8.0
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hail==0.2.132
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luigi>=3.4.0
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gnomad==0.6.4
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google-cloud-storage>=2.14.0
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aiofiles==24.1.0
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pydantic==2.8.2

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