Quickstart based integration test [VS-357] #7812
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## ah_var_store #7812 +/- ##
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| input_vcfs = input_vcfs, | ||
| input_vcf_indexes = input_vcf_indexes, | ||
| filter_set_name = "quickit", | ||
| create_filter_set_scatter_count = 20, |
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do we still need these filter params if we are turning filtering off for now (extract_do_not_filter_override) ? (The answer may totally be yes and someplace else needs that updated)
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I would defer to you on that, though I was hoping filtering wouldn't be off for too long (though maybe it will, I don't know).
| # but also for building nightly GATK jars. This wouldn't be that valuable for this current increment of work as | ||
| # using a Docker image would save maybe 10 minutes from what is currently a ~4 hour workflow, but a Docker image | ||
| # could become more compelling if a scaled down version of this test that could run more frequently was created, | ||
| # in addition to the nightly build use case mentioned above. |
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How is GATK doing this for their nightlys?
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yeah I should look into that more
| fi | ||
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| echo "All vcfs compared and matched!" | ||
| >>> |
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When we are ready to start doing fuzzy comparisons (with filtering), we could potentially use the ah_var_store docker image which has bcftools in it and do some easy selective comparisons that way. eg take two vcfs and compare only their variants as opposed to their bytes
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bcftools would also allow us to merge all of the shards into one fairly quickly which could also speed up the comparison
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| task Prepare { |
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nit: can this be something else, like "setup", just to not create any confusion with the PrepareRangesCallset step?
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Fully manual for now, also turns off filtering as that appears to be nondeterministic and this currently only does exact matching of actual to expected results.