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Fixes the issue in #475

Tested via docker, gcloud and pipelines run.
Got the same error as customer with following command on older image, but passed with new image:
pipelines run action_input.json --scopes https://www.googleapis.com/auth/genomics,https://www.googleapis.com/auth/cloud-platform --zones us-west1-b

with action_input.json:
[
{
"imageUri": "gcr.io/tural-test-runner/gcp-variant-transforms:a53a8fa653d5110ac3da0d5ed71f1147dde3fd33",
"commands": ["/opt/gcp_variant_transforms/bin/vcf_to_bq", "--project", "tural-test-runner", "--input_pattern", "gs://gcp-variant-transforms-testfiles/small_tests/valid-4.0.vcf", "--output_table", "tural-test-runner:turalds.test1800", "--runner", "DataflowRunner", "--job_name", "vcf-to-bigquery", "--temp_location", "gs://tural-test-runner/temp", "--staging_location", "gs://tural-test-runner/staging"],
}
]

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coveralls commented Apr 18, 2019

Pull Request Test Coverage Report for Build 1687

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage remained the same at 87.816%

Totals Coverage Status
Change from base Build 1683: 0.0%
Covered Lines: 7027
Relevant Lines: 8002

💛 - Coveralls


function main {
if [[ $1 == /opt/gcp_variant_transforms/bin/* ]]; then
$@

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I think you want to exec it instead so the return status is correct

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Done.

@tneymanov tneymanov merged commit 0211581 into googlegenomics:master Apr 19, 2019
@tneymanov tneymanov deleted the fix_release branch May 3, 2019 17:58
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3 participants