diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 94039c2..2c51f84 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -63,14 +63,6 @@ on:
           - conda
         required: false
 
-      workflow-root:
-        description: >-
-          Path to the root of the workflow folder (e.g. one that contains a Snakefile) to run CI on.
-          Defaults to the root of the workflow repo.
-        type: string
-        default: ${{ github.workspace }}
-        required: false
-
       artifact-name:
         description: >-
           Name to use for build results artifact uploaded at the end of the
@@ -236,7 +228,6 @@ jobs:
           python-version: "3.7"
 
       - name: Copy example data
-        working-directory: ${{ inputs.workflow-root }}
         run: |
           if [[ -d example_data ]]; then
             mkdir -p data/
@@ -246,17 +237,14 @@ jobs:
           fi
 
       - run: nextstrain build . ${{ inputs.build-args }}
-        working-directory: ${{ inputs.workflow-root }}
 
       - if: always()
         uses: actions/upload-artifact@v3
-        env:
-          workdir: ${{ inputs.workflow-root }}
         with:
           name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
           path: |
-            $workdir/auspice/
-            $workdir/results/
-            $workdir/benchmarks/
-            $workdir/logs/
-            $workdir/.snakemake/log/
+            auspice/
+            results/
+            benchmarks/
+            logs/
+            .snakemake/log/