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Fix VCF integration assertion, revert extract scatters [VS-1820] #9340

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Merged
mcovarr merged 9 commits into from
Mar 10, 2026
Merged

Fix VCF integration assertion, revert extract scatters [VS-1820] #9340

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412aecf
Fix VCF integration assertion [VS-1820]
mcovarr Mar 2, 2026
7b3b613
dockstore
mcovarr Mar 2, 2026
2bb4c5c
sus
mcovarr Mar 2, 2026
b41a2fa
dockstore
mcovarr Mar 3, 2026
41e6e9f
revert dockstore
mcovarr Mar 3, 2026
51de693
dockstore
mcovarr Mar 5, 2026
088dde0
more
mcovarr Mar 9, 2026
ca46ec9
boop
mcovarr Mar 10, 2026
24fe04a
cleanup
mcovarr Mar 10, 2026
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsExtractCallset.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -136,12 +136,12 @@ workflow GvsExtractCallset {

Int effective_scatter_count = if defined(scatter_count) then select_first([scatter_count])
else if is_wgs then
if GetNumSamplesLoaded.num_samples < 5000 then 500
if GetNumSamplesLoaded.num_samples < 5000 then 1
else if GetNumSamplesLoaded.num_samples < 20000 then 2000
else if GetNumSamplesLoaded.num_samples < 50000 then 10000
else 20000
else
if GetNumSamplesLoaded.num_samples < 5000 then 500
if GetNumSamplesLoaded.num_samples < 5000 then 1
else if GetNumSamplesLoaded.num_samples < 20000 then 1000
else if GetNumSamplesLoaded.num_samples < 50000 then 2500
else 7500
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/test/GvsQuickstartVcfIntegration.wdl
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Expand Up @@ -444,7 +444,7 @@ task AssertCostIsTrackedAndExpected {
DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
fi

if ! awk "BEGIN{ exit ($DIFF_FOUND -gt $TOLERANCE) }"
if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
then
echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
echo "1" > ret_val.txt
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