check for duplicate ids #7273
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check for duplicate ids #7273
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rsasch
approved these changes
May 26, 2021
kcibul
approved these changes
May 26, 2021
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| if [ ~{has_service_account_file} = 'true' ]; then | ||
| gcloud auth activate-service-account --key-file='~{service_account_json}' | ||
| gcloud config set project ~{project_id} |
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should we also set the environment variable here? I don't know if it's needed but just to be consistent everywhere
export GOOGLE_APPLICATION_CREDENTIALS=~{service_account_json}
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we only need to set the environment variable when the gatk tool needs to access bigquery. Also, I believe (but have not verified) that when we set it, we have to localize all input files that are not in the aou project. Meaning that if we try to pass a gs path to the GATK that is in a workspace bucket, it won't be able to read the file.
| fi | ||
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| # true if there is data in results | ||
| if [ -s duplicates ]; then |
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nice -- I learned something new!
This was referenced Mar 17, 2023
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query the partition table to see if samples have already been loaded