diff --git a/.github/workflows/phylogenetic.yaml b/.github/workflows/phylogenetic.yaml
index 2ff990e..857b021 100644
--- a/.github/workflows/phylogenetic.yaml
+++ b/.github/workflows/phylogenetic.yaml
@@ -30,6 +30,18 @@ on:
           If set, builds will be deployed to s3://nextstrain-staging/zika_trials_<trial_name>_*
         required: false
         type: string
+      sequences_url:
+        description: |
+          URL for a sequences.fasta.zst file.
+          If not provided, will use default sequences_url from phylogenetic/defaults/config_zika.yaml
+        required: false
+        type: string
+      metadata_url:
+        description: |
+          URL for a metadata.tsv.zst file.
+          If not provided, will use default metadata_url from phylogenetic/defaults/config_zika.yaml
+        required: false
+        type: string
 
 jobs:
   set_config_overrides:
@@ -39,11 +51,26 @@ jobs:
         name: Set config overrides
         env:
           TRIAL_NAME: ${{ inputs.trial_name }}
+          SEQUENCES_URL: ${{ inputs.sequences_url }}
+          METADATA_URL: ${{ inputs.metadata_url }}
         run: |
           config=""
-          if [[ "$TRIAL_NAME" ]]; then
+          if [[ "$TRIAL_NAME" || "$SEQUENCES_URL" || "$METADATA_URL" ]]; then
+
             config+="--config"
-            config+=" deploy_url='s3://nextstrain-staging/zika_trials_"$TRIAL_NAME"_'"
+
+            if [[ "$TRIAL_NAME" ]]; then
+              config+=" deploy_url='s3://nextstrain-staging/zika_trials_"$TRIAL_NAME"_'"
+            fi
+
+            if [[ "$SEQUENCES_URL" ]]; then
+              config+=" sequences_url='"$SEQUENCES_URL"'"
+            fi
+
+            if [[ "$METADATA_URL" ]]; then
+              config+=" metadata_url='"$METADATA_URL"'"
+            fi
+
           fi
 
           echo "config=$config" >> "$GITHUB_OUTPUT"