add vqsr cutoffs to GvsExtractCallset wdl; clean up dockstore yml #7209
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mmorgantaylor
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| @@ -17,6 +17,13 @@ workflow GvsExtractCallset { | |||
| String? fq_filter_set_site_table | |||
| String? fq_filter_set_tranches_table | |||
| String? filter_set_name | |||
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Can we make the corresponding changes above to default these table names given a "default_dataset" etc? We can also make them non-optional, though we would need to check that works with ExtractCohort (ie if I specify those table names, but no filter set... I mean "don't filter"... we might explode right now in that scenario)
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yeah, I'll give it a shot, we should think about what the decision-making input will be that decides whether to filter or not. right now it's whether --filter-set-info-table is input to the tool - maybe we should change that to be whether a filter set name is input? then we could have defaults for the table names like you suggest
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@kcibul how does this look to you now? i tested that it works with and without filtering in Terra (i.e. providing filter-table-name, and setting do_not_filter_override to true, respectively)
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specops issue #287
tested with defined truth sensitivities here: https://app.terra.bio/#workspaces/broad-dsp-spec-ops-fc/gvs_testing_no_sa/job_history/39f8c4ea-8e21-46d4-a6ba-8e570ce75f8b