diff --git a/.github/workflows/cromwell-test-run.yml b/.github/workflows/cromwell-test-run.yml
index d743520..7ab0d43 100644
--- a/.github/workflows/cromwell-test-run.yml
+++ b/.github/workflows/cromwell-test-run.yml
@@ -17,7 +17,7 @@ jobs:
         id: set-matrix
         run: |
           # Find all directories containing .wdl files
-          dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; | sort -u | jq -R . | jq -s | jq -c .)
+          dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; | sort -u | sed 's|^\./||' | jq -R . | jq -s | jq -c .)
           echo "Directories: $dirs"
           echo "matrix=$dirs" >> $GITHUB_OUTPUT
 
diff --git a/.github/workflows/womtools-validate.yml b/.github/workflows/womtools-validate.yml
index ecfe49d..a23c92a 100644
--- a/.github/workflows/womtools-validate.yml
+++ b/.github/workflows/womtools-validate.yml
@@ -21,7 +21,7 @@ jobs:
         id: set-matrix
         run: |
           # Find all directories containing .wdl files
-          dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; | sort -u | jq -R . | jq -s | jq -c .)
+          dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; | sort -u | sed 's|^\./||' | jq -R . | jq -s | jq -c .)
           echo "Directories: $dirs"
           echo "matrix=$dirs" >> $GITHUB_OUTPUT