[GH-1205] TDR schemas for sarscov2_illumina_full pipeline #328
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tbl3rd
approved these changes
Feb 22, 2021
| method-configuration-name | ||
| method-configuration-namespace | ||
| entity-type | ||
| entity-name) |
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Maybe create-submission should take [url workspace {:keys [mcn mcns et en] :as submission}] or sumpin?
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Good idea. I plan to change this namespace a bit and remove the url parameter too! For next change.
ehigham
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Feb 23, 2021
RR: https://broadinstitute.atlassian.net/browse/GH-1172 Historically, a workload defines an "executor" url to be the URL of cromwell/terra to submit workflows to. While this made sense for Cromwell, Terra is sufficiently different to warrant a change from this (i.e. we don't have to fear Henry's wrath if we overload it :D ). In this change, therefore, I'm fixing the firecloud api URL to "api.firecloud.org". This can be overwritten using the environment variable "WFL_FIRECLOUD_URL" or in tests via with-temporary-environment. Since the "Arrays" WDL is not available via through Dockstore in app.terra.bio, I'm disabling the arrays system tests. See https://broadinstitute.atlassian.net/browse/GH-1209 for more info. Included here is some re-working of the "firecloud" namespace, including tweaks suggested by Tom #328 (comment)
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This PR adds preliminary TDR schemas for the inputs and outputs of the sarscov2_illimina_full pipeline (a.k.a. the COVID-19 uber wdl).
As with #316, this schema is meant for testing only.
I'm yet to get the outputs for the pipeline. An ingest test will follow in a subsequent PR.