Fix Race Condition, Add Support for Extract by Array of Sample Names (ie from a Sample Set) #7917
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@@ Coverage Diff @@
## ah_var_store #7917 +/- ##
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Coverage ? 86.288%
Complexity ? 35194
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Files ? 2170
Lines ? 164888
Branches ? 17785
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Hits ? 142278
Misses ? 16288
Partials ? 6322 |
| call write_array_task { | ||
| input: | ||
| input_array = select_first([cohort_sample_names_array]), | ||
| docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:305.0.0" |
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Pinning cloud SDK versions can help avoid bugs but this particular one is ~2 years old
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Yep - I'm just taking the same version we use in other parts of the pipelines. We may be old but at least were consistent 😆
| @@ -34,10 +35,22 @@ workflow GvsExtractCohortFromSampleNames { | |||
| File? gatk_override | |||
| } | |||
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| # writing the array to a file has to be done in a task | |||
| # https://support.terra.bio/hc/en-us/community/posts/360071465631-write-lines-write-map-write-tsv-write-json-fail-when-run-in-a-workflow-rather-than-in-a-task | |||
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yeah -- def a bummer, but seems to be the way it is
| @@ -8,7 +8,8 @@ import "GvsExtractCallset.wdl" as GvsExtractCallset | |||
| workflow GvsExtractCohortFromSampleNames { | |||
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| input { | |||
| File cohort_sample_names | |||
| File? cohort_sample_names | |||
| Array[String]? cohort_sample_names_array | |||
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maybe a comment here that cohort_sample_names will be ignored if cohort_sample_names_array is defined?
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