Add a github action to run womtool validation on all WDLs #7822
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## ah_var_store #7822 +/- ##
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Coverage ? 86.280%
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Hits ? 142221
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Fixed two wdls that were failing to validate
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| @@ -151,7 +151,7 @@ workflow JointCallExomeCNVs { | |||
| } | |||
| Array[String] subset_arr = select_all(subset) | |||
| Array[String] subset_index_arr = select_all(subset_indexes) | |||
| Array[String] failed_samples = select_all(failed) | |||
| Array[String] failed_samples_arr = select_all(failed) | |||
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Changed the name of this (internal) variable as it is also defined as an output and was failing validation for that reason
| @@ -0,0 +1,1070 @@ | |||
| version 1.0 | |||
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Completely added this file to make JointGenotyping.wdl validate (it couldn't find the file, which is zipped up in a dependencies zip).
Co-authored-by: Miguel Covarrubias <[email protected]>
| .idea | ||
| ) | ||
| declare -r CROMWELL=https://github.com/broadinstitute/cromwell | ||
| declare -r WOMTOOL=$CROMWELL/releases/download/78/womtool-78.jar |
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Sorry for the drive-by, but I wanted to point out that there is already a gradle task and github action that we use to do something very similar (install cromwell and womtool to validate and test the autogenerated WDLs). It would be good to integrate with that, or at least use the same cromwell and womtool versions for all the WDLs in the repo (not sure how far back this branch is). BTW, I think the existing tasks use pretty old cromwell and womtool versions, but its probably time to update those. Either way I'll make a PR to update those, but just wanted to make sure you knew about the existing machinery.
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OOC does this PR stand in its current form or is #7826 going to be backported / cherry picked to |
Added a github action to run womtool validation on all WDLs
Also fixed two wdls that were failing validation.