added docstore bindings to the permutect wdls

broadinstitute · Jan 21, 2025 · 36ae7f2 · 36ae7f2
1 parent 15644f2
commit 36ae7f2
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Showing 3 changed files with 38 additions and 3 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -136,3 +136,36 @@ workflows:
              - master
          tags:
              - /.*/
+   - name: permutect_call_variants_with_uda
+     subclass: WDL
+     primaryDescriptorPath: /scripts/permutect/call_variants_with_uda.wdl
+#     testParameterFiles:
+#       - /scripts/pathseq/wdl/pathseq_pipeline_template.json
+     filters:
+       branches:
+         - master
+         - je_updateCondaEnvironment
+       tags:
+         - /.*/
+   - name: permutect_make_training_dataset
+       subclass: WDL
+       primaryDescriptorPath: /scripts/permutect/make_training_dataset.wdl
+       #     testParameterFiles:
+       #       - /scripts/pathseq/wdl/pathseq_pipeline_template.json
+       filters:
+         branches:
+           - master
+           - je_updateCondaEnvironment
+         tags:
+           - /.*/
+   - name: permutect_train_base_model
+       subclass: WDL
+       primaryDescriptorPath: /scripts/permutect/permutect_train_base_model.wdl
+       #     testParameterFiles:
+       #       - /scripts/pathseq/wdl/pathseq_pipeline_template.json
+       filters:
+         branches:
+           - master
+           - je_updateCondaEnvironment
+         tags:
+           - /.*/
diff --git a/scripts/permutect/call_variants_with_uda.wdl b/scripts/permutect/call_variants_with_uda.wdl
@@ -7,9 +7,9 @@ version 1.0
 # note that the artifact model can be trained before the Mutect2 workflow runs FilterMutectCalls
 
 import "https://api.firecloud.org/ga4gh/v1/tools/davidben:mutect2/versions/18/plain-WDL/descriptor" as m2
-import "https://api.firecloud.org/ga4gh/v1/tools/emeryj:permutect-uda-dataset.modified/versions/1/plain-WDL/descriptor" as uda
-import "https://api.firecloud.org/ga4gh/v1/tools/emeryj:permutect-train-artifact-model.modified/versions/2/plain-WDL/descriptor" as training
-import "https://api.firecloud.org/ga4gh/v1/tools/emeryj:permutect-call-variants.modified/versions/1/plain-WDL/descriptor" as calling
+import "permutect-uda-dataset.wdl" as uda
+import "permutect-train-artifact-model.wdl" as training
+import "permutect-call-variants.wdl" as calling
 
 workflow CallVariantsWithUDA {
     input {

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/permutect/PermutectTrainBaseModel.java b/src/main/java/org/broadinstitute/hellbender/tools/permutect/PermutectTrainBaseModel.java
@@ -70,4 +70,6 @@ protected Object doWork() {
                 null,
                 pythonifiedArguments);
     }
+
+
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -70,4 +70,6 @@ protected Object doWork() { @@
                     null,
                     pythonifiedArguments);
         }
     }