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populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
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Removing the necessity of having large_cohorts.output_versions in config files #744

Closed michael-harper closed 4 months ago

michael-harper commented 4 months ago

Fixes issue https://github.com/populationgenomics/production-pipelines/issues/737

Have added the new config_retrieve() function with a default=None instead of nested .get() methods.

Batch that succeeded: https://batch.hail.populationgenomics.org.au/batches/447653/jobs/1 (I cancelled the subsequent batch but the driver kicked). Compared to failed batch linked in the issue https://batch.hail.populationgenomics.org.au/batches/445312/jobs/1 that has the same config