add the skylab tests to the pr tests/nightly tests (#816)

*run all pipelines in smart tests
broadinstitute · Sep 9, 2022 · d8a0315 · d8a0315
1 parent d7e439c
commit d8a0315
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/scripts/get_changed_pipeline_worklow_test_args.sh b/scripts/get_changed_pipeline_worklow_test_args.sh
@@ -68,13 +68,13 @@ function pipeline_to_args() {
       if [[ "${test}" == "Scientific" ]]; then
         echo CloudWorkflow -p MultiSampleSmartSeq2 -e ${env} -t Plumbing -b ${truth} ${uncached}
       else
-        continue
+        echo CloudWorkflow -p MultiSampleSmartSeq2 ${common_args}
       fi;;
     MultiSampleSmartSeq2SingleNucleus)
       if [[ "${test}" == "Scientific" ]]; then
         echo CloudWorkflow -p MultiSampleSmartSeq2SingleNucleus -e ${env} -t Plumbing -b ${truth} ${uncached}
       else
-        continue
+        echo CloudWorkflow -p MultiSampleSmartSeq2SingleNucleus ${common_args}
       fi;;
     Optimus)
       echo CloudWorkflow -p Optimus ${common_args};;
@@ -86,13 +86,13 @@ function pipeline_to_args() {
       if [[ "${test}" == "Scientific" ]]; then
         echo CloudWorkflow -p scATAC -e ${env} -t Plumbing -b ${truth} ${uncached}
       else
-        continue
+        echo CloudWorkflow -p scATAC ${common_args}
       fi;;
     SmartSeq2SingleSample)
       if [[ "${test}" == "Scientific" ]]; then
         echo CloudWorkflow -p SmartSeq2SingleSample -e ${env} -t Plumbing -b ${truth} ${uncached}
       else
-        continue
+        echo CloudWorkflow -p SmartSeq2SingleSample ${common_args}
       fi;;
     TargetedSomaticSingleSample)
       continue;;
@@ -102,7 +102,7 @@ function pipeline_to_args() {
       if [[ "${test}" == "Scientific" ]]; then
         echo CloudWorkflow -p VariantCalling -e ${env} -t Plumbing -b ${truth} ${uncached}
       else
-        continue
+         echo CloudWorkflow -p VariantCalling ${common_args}
       fi;;
     WholeGenomeGermlineSingleSample)
       echo CloudWorkflow -p WholeGenomeGermlineSingleSample ${common_args};;
@@ -112,8 +112,8 @@ function pipeline_to_args() {
       else
         continue
       fi;;
-    UltimaGenomicsGermlineSingleSample)
-      echo CloudWorkflow -p UltimaGenomicsGermlineSingleSample ${common_args};;
+    UltimaGenomicsWholeGenomeGermline)
+      echo CloudWorkflow -p UltimaGenomicsWholeGenomeGermline ${common_args};;
     UltimaGenomicsJointGenotyping)
       echo CloudWorkflow -p UltimaGenomicsJointGenotyping ${common_args};;
   esac

diff --git a/...a_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/PipelineTestType.scala b/...a_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/PipelineTestType.scala
@@ -119,7 +119,7 @@ object PipelineTestType extends Enum[PipelineTestType] {
       extends PipelineTestType(
         "TestUltimaGenomicsWholeGenomeGermline",
         "UltimaGenomicsWholeGenomeGermline",
-        "/broad/dna_seq/germline/single_sample/UGWGS/"
+        "/broad/dna_seq/germline/single_sample/ugwgs/"
       )
   case object ValidateChip
       extends PipelineTestType(