WDLize GvsPrepareCallset (briefly known as CreateCohortTable) #7200
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mmorgantaylor
commented
Apr 13, 2021
.dockstore.yml
Outdated
| branches: | ||
| - master | ||
| - ah_var_store | ||
| - mmt_ngs_cohort_extract_wdl |
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remove before merging
RoriCremer
reviewed
Apr 13, 2021
| @@ -68,7 +72,8 @@ task CreateCohortTableTask { | |||
| --destination_table ~{destination_cohort_table_name_final} \ | |||
| --fq_cohort_sample_names ~{fq_cohort_sample_table_final} \ | |||
| --query_project ~{query_project_final} \ | |||
| --fq_sample_mapping_table ~{fq_sample_mapping_table_final} | |||
| --fq_sample_mapping_table ~{fq_sample_mapping_table_final} \ | |||
| $SA_ARGS | |||
RoriCremer
reviewed
Apr 13, 2021
| String? fq_cohort_sample_table | ||
| String? fq_sample_mapping_table | ||
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| File? service_account_json |
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is this still defined as a File even if it's just a path to a json in GCP?
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as Kris pointed out, since it's a file, it'll localize, so we can just pass it straight into python. tested!
RoriCremer
approved these changes
Apr 13, 2021
kcibul
reviewed
Apr 14, 2021
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| if [ ~{has_service_account_file} = 'true' ]; then | ||
| SA_FILENAME="sa_key.json" | ||
| gsutil cp "~{service_account_json}" $SA_FILENAME |
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If this is declared as aFile above, won't it already be copied down to the VM now and the path be a local path?
kcibul
reviewed
Apr 14, 2021
| @@ -0,0 +1,14 @@ | |||
| if [ $# -lt 1 ]; then | |||
| echo "USAGE: ./build_docker.sh [DOCKER_TAG_STRING]" | |||
kcibul
approved these changes
Apr 14, 2021
mmorgantaylor
commented
Apr 14, 2021
mmorgantaylor
changed the title
This was referenced Mar 17, 2023
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specops issue #273: https://github.com/broadinstitute/dsp-spec-ops/issues/273
ngs_cohort_extract.py->create_cohort_extract_data_table.pyUser does not have bigquery.jobs.create permission in project specops-variantstore-sa-tests.