Benb/use metadata as source of family table load #936
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bpblanken
commented
Oct 28, 2024
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| # Fetch family guids from pedigree |
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The specific failure was a family existing in the pedigree, failing a check and thus being excluded from the rest of the pipeline, but being present on the project table from a different callset.
hanars
reviewed
Oct 28, 2024
| family_guids_in_project_table & families_guids_in_pedigree | ||
| def run(self): | ||
| ht = hl.read_matrix_table( | ||
| remapped_and_subsetted_callset_path( |
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just sanity checking that this works for AnVIL loading where we don't have remaps (or usually subsets)
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yeah the same file gets generated, we just run a "subset" that has all families in it.
hanars
approved these changes
Oct 28, 2024
bpblanken
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Nov 5, 2024
* 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 <[email protected]>
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