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Ensure rc/stdout/stderr upload when task outputs missing when using AWS Batch #7826

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Ensure rc/stdout/stderr upload when task outputs missing when using AWS Batch #7826

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bdc6b6a
feat: upload rc, stderr and stdout on failure
sberss Nov 25, 2025
a6c1279
chore: update changelog
sberss Nov 25, 2025
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,9 @@ The index `IX_METADATA_ENTRY_WEU_CFQN_JSI_JRA_MK` is added to `METADATA_ENTRY`.

This index supports planned metadata API enhancements that enable querying at granular scopes, namely calls, shards, and attempts.

### AWS Batch
* Fixed an issue where job failures before all outputs were written would cause delocalization to fail, preventing the upload of return code, stdout, and stderr files needed for debugging.

## 91 Release Notes

#### Removal of Google LifeSciences backend code
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12 changes: 8 additions & 4 deletions supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
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Expand Up @@ -577,7 +577,6 @@ final case class AwsBatchJob(
replaced.patch(insertionPoint, preamble, 0) +
s"""
|{
|set -e
|# (re-)add tags to include added volumes:
|if [[ "${doTagging}" == "true" ]]; then
| echo "*** TAGGING RESOURCES ***"
Expand All @@ -588,15 +587,20 @@ final case class AwsBatchJob(
|DELOCALIZATION_FAILED=0
|$outputCopyCommand
|echo "DELOCALIZATION RESULT: $$DELOCALIZATION_FAILED"
|rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename} 2>/dev/null) || rc=1
|if [[ $$DELOCALIZATION_FAILED -eq 1 ]]; then
| echo '*** DELOCALIZATION FAILED ***'
| echo '*** EXITING WITH RETURN CODE 1***'
| exit 1
| if [[ "$$rc" -eq 0 ]]; then
| echo '*** EXITING WITH RETURN CODE 1 ***'
| exit 1
| else
| echo "*** EXITING WITH ORIGINAL RETURN CODE $$rc ***"
| exit $$rc
| fi
|else
| echo '*** COMPLETED DELOCALIZATION ***'
|fi
|echo '*** EXITING WITH RETURN CODE ***'
|rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
|echo $$rc
|exit $$rc
|}
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