💚 Update pytest command and disk size calculation

lmtani · Dec 18, 2023 · a9aac45 · a9aac45
1 parent 7a0df80
commit a9aac45
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -67,12 +67,12 @@ jobs:
         run: pip install -r tests/requirements.txt
 
       - name: Run test ${{ matrix.tag }}
-        run: pytest --tag ${{ matrix.tag }} --basetemp /tmp/ci tests/tasks
+        run: pytest --git-aware --tag ${{ matrix.tag }} --basetemp temp-dir tests/tasks
 
       - uses: actions/upload-artifact@v4
         with:
           name: miniwdl-command
-          path: /tmp/ci/*/_LAST/command
+          path: temp-dir/**/command
 
   release:
     needs: [test]

diff --git a/tasks/clair3/haploid.wdl b/tasks/clair3/haploid.wdl
@@ -15,6 +15,8 @@ task Clair3Haploid {
         Boolean stub = false
     }
 
+    Int disk_size = ceil((size(alignment, "GB") + size(reference, "GB") + size(model_tar, "GB")) * 2)
+
     command <<<
     set -e
 
@@ -53,6 +55,7 @@ task Clair3Haploid {
         docker: "docker.io/hkubal/clair3:v1.0.4"
         cpu: threads
         memory: "8G"  # TODO: check if it's enough
+        disks: "local-disk " + disk_size + " HDD"
     }
 
     output {