EVA-3457 - Split variant load #195
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…istics calculation
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| pipeline_parameters += " --spring.batch.job.names=calculate-statistics-job" | ||
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| pipeline_parameters += " --input.vcf.aggregation=" + aggregation.toString().toUpperCase() |
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If I'm understanding the old job configurations correctly, we should only run statistics calculation for genotyped vcf.
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That's a good point and one I was not aware of.
I'm a bit surprised by this considering that there are both variant level and study level statistics in the mongodb database. Maybe the study level is calculated in the Variant Load step.
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I wonder if this is why this assertion passes in your test, even though the stats step hasn't been run...
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Yes that might be something else to investigate
apriltuesday
approved these changes
Jan 15, 2024
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Split the variant load nextflow process into
Also remove the option to run annotation only.