Resolved issue: gatk-launch appends as needed to GATK_GCS_STAGING #1338

[MartonKN]

Resolved the issue of adding gs:// to the beginning and / to the end of the environment variable GATK_GCS_STAGING. Tested it locally.

[codecov-io]

Codecov Report

Merging #5452 into master will decrease coverage by 0.019%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5452       +/-   ##
===============================================
- Coverage     87.006%   86.987%   -0.019%     
- Complexity     31175     31200       +25     
===============================================
  Files           1908      1909        +1     
  Lines         144008    144184      +176     
  Branches       15927     15951       +24     
===============================================
+ Hits          125296    125422      +126     
- Misses         12955     12994       +39     
- Partials        5757      5768       +11

Impacted Files	Coverage Δ	Complexity Δ
...ataSources/xsv/LocatableXsvFuncotationFactory.java	79.452% <0%> (-3.647%)	21% <0%> (-1%)
...bender/utils/GATKProtectedVariantContextUtils.java	67.005% <0%> (-3.325%)	66% <0%> (+1%)
...oadinstitute/hellbender/engine/FeatureManager.java	84.071% <0%> (-3.085%)	49% <0%> (ø)
...tils/annotatedinterval/AnnotatedIntervalCodec.java	77.778% <0%> (-1.533%)	18% <0%> (ø)
...dataSources/gencode/GencodeFuncotationFactory.java	86.536% <0%> (-1.494%)	230% <0%> (+1%)
...er/tools/funcotator/FuncotatorIntegrationTest.java	84.567% <0%> (-1.401%)	111% <0%> (ø)
...broadinstitute/hellbender/engine/FeatureInput.java	93.056% <0%> (-1.311%)	18% <0%> (ø)
...decs/xsvLocatableTable/XsvLocatableTableCodec.java	81.675% <0%> (-1.041%)	66% <0%> (+6%)
...institute/hellbender/engine/FeatureDataSource.java	76.471% <0%> (-0.973%)	42% <0%> (ø)
...te/hellbender/utils/genotyper/ReadLikelihoods.java	89.981% <0%> (-0.16%)	150% <0%> (+7%)
... and 10 more

[davidbenjamin]

@MartonKN A cool github trick is that in your description of the PR (I'm not sure whether it has to be the first comment on this page) you should write: Closes #1338. Then when this PR is merged it will automatically close the issue. Also, it will make a useful cross-referencing link to the issue.

[davidbenjamin]

One suggestion.

[davidbenjamin]

staging.startswith("gs://") would be clearer.

[davidbenjamin]

Back to @MartonKN.

[davidbenjamin]

@MartonKN You can merge once tests pass.

[MartonKN]

Closes #1338

[MartonKN]

Thank you, @davidbenjamin

[MartonKN]

Closes #1338 on Github