diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 51391772..fe93b6a9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -23,6 +23,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          depth: 0
       - name: Formatting
         uses: super-linter/super-linter@v5.7.2
         env:
diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml
index f6a26ad4..42265aca 100644
--- a/workflow/envs/pangolin.yaml
+++ b/workflow/envs/pangolin.yaml
@@ -4,3 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - pangolin =4.3
+  - snakemake-minimal=7.24.0 # TODO keep until https://github.com/bioconda/bioconda-recipes/pull/42192 and we can pin to 4.3.1 above
diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml
index d88fde2c..32c7a4d3 100644
--- a/workflow/envs/spades.yaml
+++ b/workflow/envs/spades.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - spades =3.15
+  - spades =4.0