Quickstart based integration test [VS-357] #7812
Conversation
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7812 +/- ##
================================================
Coverage ? 86.303%
Complexity ? 35194
================================================
Files ? 2170
Lines ? 164837
Branches ? 17774
================================================
Hits ? 142260
Misses ? 16254
Partials ? 6323 |
| input_vcfs = input_vcfs, | ||
| input_vcf_indexes = input_vcf_indexes, | ||
| filter_set_name = "quickit", | ||
| create_filter_set_scatter_count = 20, |
There was a problem hiding this comment.
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)
There was a problem hiding this comment.
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. |
There was a problem hiding this comment.
How is GATK doing this for their nightlys?
There was a problem hiding this comment.
yeah I should look into that more
| fi | ||
|
|
||
| echo "All vcfs compared and matched!" | ||
| >>> |
There was a problem hiding this comment.
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
There was a problem hiding this comment.
bcftools would also allow us to merge all of the shards into one fairly quickly which could also speed up the comparison
| } | ||
| } | ||
|
|
||
| task Prepare { |
There was a problem hiding this comment.
nit: can this be something else, like "setup", just to not create any confusion with the PrepareRangesCallset step?
mcovarr
force-pushed
the
vs_357_quickstart_integration
branch
from
1b6435a to
3813472
Compare
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.