chore: checkout full history for formatting (#668)

* chore: checkout full history for formatting * force latest pangolin * work around pangolin dependency issues * Update spades.yaml --------- Co-authored-by: Alexander Thomas <[email protected]> Co-authored-by: Alex Thomas <[email protected]>
IKIM-Essen · Oct 17, 2024 · b8c5c44 · b8c5c44
1 parent 5c5a108
commit b8c5c44
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diff --git 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/[email protected]
         env:

diff --git 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
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - spades =3.15
+  - spades =4.0