take sample name as a param #7236
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| @@ -5,6 +5,7 @@ workflow GvsImportGenomes { | |||
| input { | |||
| Array[File] input_vcfs | |||
| Array[File] input_vcf_indexes | |||
| Array[String] research_ids | |||
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Maybe let's call this external_sample_name or something like that? research_ids is pretty specific to AoU
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Also -- can you update the example json (GvsImportGenomes.example.inputs.json)
| @@ -24,6 +25,9 @@ workflow GvsImportGenomes { | |||
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| String docker_final = select_first([docker, "us.gcr.io/broad-gatk/gatk:4.1.7.0"]) | |||
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| # how do i return an error if the lengths are not equal? | |||
| # if (length(input_vcfs) != length(input_vcf_indexes) != length(research_ids)) | |||
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I think if you just exit 1 from bash here, that would cause the overall task to fail
| doc = "Sample id", | ||
| optional = true) | ||
| public Long sampleIdParam; | ||
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| @Argument(fullName = "sample-name", | ||
| shortName = "SN", | ||
| doc = "Sample id", |
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Some docs here would be really helpful I think for the constellation of parameters around sample-name, gvs-sample-id, sample-name-mapping (maybe even the same comment for all of these parameters).
scripts/variantstore/README.md
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| After using the json file to auth as that service account, you can query the | ||
| `region-us`.INFORMATION_SCHEMA.JOBS_BY_USER table to narrow down the query you are interested in. | ||
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| gcloud auth activate-service-account --key-file=aou_wgs_vumc_prod.json |
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maybe change the json key name here, I'm nervous about having AOU specific details checked into a public repo
scripts/variantstore/README.md
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| gcloud auth activate-service-account --key-file=aou_wgs_vumc_prod.json | ||
| # use queries like this to narrow down the time window of the queries you are interested in | ||
| bq --project_id aou-genomics-curation-prod query --use_legacy_sql=false 'select total_bytes_billed, job_id, creation_time, start_time, query from `region-us`.INFORMATION_SCHEMA.JOBS_BY_USER where creation_time > "2021-04-16 00:00:00" and creation_time < "2021-04-18 00:00:00" and total_bytes_billed > 1 order by creation_time asc limit 100' |
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same thing for the project IDs
This also start the mark down for how to find cost info for the aou prod project