diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 000ec5c..0650dbe 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -11,4 +11,4 @@ jobs:
     # conform since this is a collaborative repo with an external group.
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0
     with:
-      build-args: --configfile config/gisaid.yaml -pf test_target
+      build-args: --snakefile gisaid/Snakefile -pf test_target
diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml
index c4ed772..6ab0cd4 100644
--- a/.github/workflows/phylogenetic-fauna.yaml
+++ b/.github/workflows/phylogenetic-fauna.yaml
@@ -88,7 +88,7 @@ jobs:
           --memory 28800mib \
           . \
             deploy_all \
-            --configfile config/gisaid.yaml \
+            --snakefile gisaid/Snakefile \
             --config "${config[@]}"
 
       env: |
diff --git a/.github/workflows/phylogenetic-ncbi.yaml b/.github/workflows/phylogenetic-ncbi.yaml
index 2536ba1..5a69ef7 100644
--- a/.github/workflows/phylogenetic-ncbi.yaml
+++ b/.github/workflows/phylogenetic-ncbi.yaml
@@ -95,7 +95,7 @@ jobs:
           --memory 28800mib \
           . \
             deploy_all \
-            --configfile config/h5n1-cattle-outbreak.yaml \
+            --snakefile h5n1-cattle-outbreak/Snakefile \
             --config "${config[@]}"
 
       env: |