Next major release (v3.0.0-alpha1) #185
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williamrowell
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- remove the deepvariant_version option and hard-code the default into the subworkflow - remove the custom_deepvariant_model_tar option - update the version to 1.8.0 - modify task command calls to 1.8.0 options - use generic tfrecord filenames Remove the pharmcat_version option and provide the default directly within the subworkflow.
Update to DeepVariant v1.8.0
PEDigree file syntax is generated directly within WDL for each sample independently. PED files are written within tasks by `write_tsv()` by concatenating sample lines. `is_duo_kid` and `is_trio_kid` arrays are generated for convenience in preparation for duo-/trio-specific secondary/tertiary analyses. Move phenotype lookup to tertiary subworkflow. Adjust tests for changes to write_phrank. Fix write_phrank test. If sex cannot be inferred by mosdepth, output is empty string. Change `pedigree_sex["UNKNOWN"]` to `pedigree_sex[""]`.
Feature/colors-v1.2
…gree Feature/refactor-pedigree
williamrowell
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