Fix empty output files bug

[paulineribeyre]

Link to JIRA ticket if there is one:

New Features

Breaking Changes

Bug Fixes

• Fix bug: empty output files when downloaded by Nextflow (through the AWS SDK for Java)

Improvements

Dependency updates

Deployment changes

[github-actions]

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

[coveralls]

Coverage Report for CI Build 31829493650

Coverage decreased (-0.4%) to 84.274%

Details

• Coverage decreased (-0.4%) from the base build.
• Patch coverage: No coverable lines changed in this PR.
• 29 coverage regressions across 1 file.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

29 previously-covered lines in 1 file lost coverage.

File	Lines Losing Coverage	Coverage
routes/s3.py	29	74.88%

---

Coverage Stats

Relevant Lines:	1170
Covered Lines:	986
Line Coverage:	84.27%
Coverage Strength:	0.84 hits per line

---

💛 - Coveralls

[george42-ctds]

Looks good

[github-actions]

Integration Tests on Kind

filepath	passed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	28	2	30
TOTAL	28	2	30

[github-actions]

Integration Tests

Test summary after running integration tests

filepath	passed	failed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	28	1	1	30
TOTAL	28	1	1	30

Test summary after rerunning failed integration tests

filepath	passed	SUBTOTAL
tests/test_gen3_workflow.py	1	1
TOTAL	1	1

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here