Restore array output in gCNV WDLs for efficient postprocessing. #5490
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@asmirnov239 may want to look things over to make sure I haven't screwed anything up, as well! |
Codecov Report
@@ Coverage Diff @@
## master #5490 +/- ##
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- Coverage 87.081% 87.081% -<.001%
- Complexity 31478 31482 +4
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Files 1929 1930 +1
Lines 145041 145052 +11
Branches 16074 16074
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+ Hits 126303 126312 +9
Misses 12891 12891
- Partials 5847 5849 +2
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Just a reminder to @vruano, @asmirnov239, and myself that we should probably get this (and any other gCNV WDL improvements) in before 4.1. |
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I'll kick off a test run on FC soon (the queue is currently a bit backed up)... |
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@vruano @asmirnov239 I think this is good to go, please review. |
asmirnov239
approved these changes
Jan 8, 2019
src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
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Reverts the reversion in #5225, this time addressing the lexicographical ordering issue in #5217 at the WDL level by simply renaming gCNV output at the command line. If desired, we can eventually change gCNV itself to output filenames that are robust against lexicographic ordering, but this is low priority in my opinion.
@vruano this is what we discussed last week. Tests pass on Travis, and I'm pretty sure this fix should work OK, but I have not done an actual run with enough samples to see the fix in action. Can I assign you to review once I get a chance to do this?
EDIT: Also went ahead and rolled an older PR #5304 into this one so I can test both at the same time.
Closes #4724.