maybe the branches are the problem

broadinstitute · Jan 21, 2025 · f78d4a1 · f78d4a1
1 parent 36ae7f2
commit f78d4a1
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Showing 3 changed files with 20 additions and 20 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -141,31 +141,31 @@ workflows:
      primaryDescriptorPath: /scripts/permutect/call_variants_with_uda.wdl
 #     testParameterFiles:
 #       - /scripts/pathseq/wdl/pathseq_pipeline_template.json
-     filters:
-       branches:
-         - master
-         - je_updateCondaEnvironment
-       tags:
-         - /.*/
+#     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:
-           - /.*/
+#       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:
-           - /.*/
+#       filters:
+#         branches:
+#           - master
+#           - je_updateCondaEnvironment
+#         tags:
+#           - /.*/
diff --git a/scripts/permutect/permutect_edit_dataset.wdl b/scripts/permutect/permutect_edit_dataset.wdl
@@ -52,7 +52,7 @@ task EditDataset {
         set -e
 
         gatk PermutectEditDataset \
-            --train-tar ~{train_tar} \
+            --train-tar ~{sep=" --train-tar " + tdrain_tar} \
             --chunk-size ~{chunk_size} \
             {" --source " + new_source} \
             --dataset-edit ~{edit_type} \

diff --git a/scripts/permutect/permutect_make_uda_dataset.wdl b/scripts/permutect/permutect_make_uda_dataset.wdl
@@ -75,7 +75,7 @@ task EditDataset {
         set -e
 
         gatk PermutectEditDataset \
-            --train-tar ~{sep=' ' train_tar} \
+            --train-tar ~{sep=' --train-tar ' train_tar} \
             --chunk-size ~{chunk_size} \
             ~{" --source " + new_source} \
             --dataset-edit ~{edit_type} \