[AoU DRC] Support uppercase site_ids for reblocking #7929
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.dockstore.yml
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| @@ -73,6 +73,7 @@ workflows: | |||
| branches: | |||
| - master | |||
| - ah_var_store | |||
| - mmt_aou_site_id_fix | |||
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to remove before merging, but keeping in case changes are requested
| (if select_first([site_id]) == "bcm" then "gs://prod-genomics-data-baylor/" else | ||
| (if select_first([site_id]) == "uw" then "gs://prod-genomics-data-northwest/" else "null" ))) | ||
| else "" | ||
| # janky lower |
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please someone tell me a better way to do this
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I couldn't find a way. If no one else can, I would just add a comment that this is WDL for .toLowerCase().
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7929 +/- ##
================================================
Coverage ? 86.288%
Complexity ? 35194
================================================
Files ? 2170
Lines ? 164888
Branches ? 17785
================================================
Hits ? 142278
Misses ? 16288
Partials ? 6322 |
| (if select_first([site_id]) == "bcm" then "gs://prod-genomics-data-baylor/" else | ||
| (if select_first([site_id]) == "uw" then "gs://prod-genomics-data-northwest/" else "null" ))) | ||
| else "" | ||
| # janky lower |
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I couldn't find a way. If no one else can, I would just add a comment that this is WDL for .toLowerCase().
| @@ -77,7 +81,7 @@ task ReblockAndCopy { | |||
| set -x | |||
|
|
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| if [ ~{site_id} -a ~{dir} == "null" ]; then | |||
| echo "dir is not set to a valid value: ~{dir}. check site_id - only valid values are ['bi', 'bcm', 'uw']" | |||
| echo "dir is not set to a valid value. site_id is ~{site_id}. check site_id - only valid values are ['bi', 'bcm', 'uw']" | |||
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nit for clarity (feel free to finesse)
| echo "dir is not set to a valid value. site_id is ~{site_id}. check site_id - only valid values are ['bi', 'bcm', 'uw']" | |
| echo "The additional output directory for the reblocked gVCFs can not set to a valid value because the site_id is '~{site_id}' and the only valid values are ['bi', 'bcm', 'uw']." |
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thank you! this is way better
| else "" | ||
| # this is WDL for .toLowerCase() for the three possible site codes | ||
| String site_id_lower = if defined(site_id) then ( | ||
| sub(sub(sub(select_first([site_id]), "BI", "bi"), "BCM", "bcm"), "UW", "uw") |
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omg this hurts, but I understand
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i agree, i am embarrassed
This PR modifies the AoU-specific WDL
GvsAoUReblockGvcfto support processing samples whose site_ids (usually lowercase) were sent in as uppercase.