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Update Spark scripts to reflect changes from #5386 and #5127. #5415

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merged 1 commit into from
Dec 10, 2018
Merged

Update Spark scripts to reflect changes from #5386 and #5127. #5415

merged 1 commit into from
Dec 10, 2018

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tomwhite
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@tomwhite tomwhite requested a review from lbergelson November 15, 2018 15:50
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Codecov Report

Merging #5415 into master will increase coverage by 0.003%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5415       +/-   ##
===============================================
+ Coverage     87.029%   87.031%   +0.003%     
- Complexity     30454     30456        +2     
===============================================
  Files           1853      1853               
  Lines         140995    140995               
  Branches       15518     15518               
===============================================
+ Hits          122706    122710        +4     
+ Misses         12648     12645        -3     
+ Partials        5641      5640        -1
Impacted Files Coverage Δ Complexity Δ
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java 60% <0%> (ø) 2% <0%> (ø) ⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java 81.098% <0%> (+0.61%) 42% <0%> (ø) ⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java 80% <0%> (+30%) 3% <0%> (+2%) ⬆️

lbergelson
lbergelson approved these changes Dec 3, 2018
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@tomwhite This looks fine except that these arguments should be kebab cased... I opened an issue to fix that. We can either merge this and then update it again when we fix that, or fix that before we merge this. Up to you.

scripts/spark_eval/exome_md-bqsr-hc_hdfs.sh
time_gatk "BQSRPipelineSpark -I hdfs:///user/$USER/exome_spark_eval/out/markdups-sharded -O hdfs:///user/$USER/exome_spark_eval/out/bqsr-sharded --sharded-output true -R hdfs:///user/$USER/exome_spark_eval/Homo_sapiens_assembly18.fasta --known-sites hdfs://${HDFS_HOST_PORT}/user/$USER/exome_spark_eval/dbsnp_138.hg18.vcf" 8 8 32g 4g
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It seems like we missed kebabing these arguments. We should fix that... I opened #5478. (and related #5479

@lbergelson lbergelson assigned tomwhite and unassigned lbergelson Dec 3, 2018
@tomwhite tomwhite merged commit 1de11f1 into master Dec 10, 2018
@tomwhite tomwhite deleted the tw_update_spark_scripts branch December 10, 2018 14:56
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@lbergelson lbergelson lbergelson approved these changes

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@tomwhite @codecov-io @lbergelson