checking and altering path for testing

ssi-dk · Nov 13, 2024 · 3f310c4 · 3f310c4
1 parent 101db11
commit 3f310c4
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Showing 2 changed files with 2 additions and 7 deletions.
diff --git a/.github/workflows/bifrost_sp_ecoli_workflow.yml b/.github/workflows/bifrost_sp_ecoli_workflow.yml
@@ -78,11 +78,6 @@ jobs:
           git clone https://github.com/ssi-dk/bifrost_test_data.git;
           cd bifrost_test_data/samples;
           bash download_S1.sh
-      
-      - name: List files in test directory
-        run: |
-          ls -lh /home/runner/work/${{ github.event.repository.name }}/${{ github.event.repository.name }}
-          pwd
 
       - name: List all files recursively
         run: |
@@ -94,4 +89,4 @@ jobs:
           --env BIFROST_DB_KEY=${{ secrets.MONGODB_ATLAS_CONNECTION }}/bifrost_test \
           -v /home/runner/work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/bifrost_test_data:/bifrost/test_data \
           ${{ github.event.repository.name }} \
-          bash -c "pip list && pytest /bifrost/components/${{ github.event.repository.name }}/test/test_*.py"
+          bash -c "pip list && pytest /home/runner/work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/test"
diff --git a/test/test_simple.py b/test/test_simple.py
@@ -30,7 +30,7 @@ class TestBifrostMinReadCheck:
     bifrost_install_dir = os.environ["BIFROST_INSTALL_DIR"]
 
     # test_dir = "/bifrost/test_data/output/test__whats_my_species/"
-    test_dir = f"{bifrost_install_dir}/bifrost/test_data/output/test__whats_my_species/"
+    test_dir = f"{bifrost_install_dir}/bifrost/test_data/output/test_bifrost_sp_ecoli/"
     r1 = f"{bifrost_install_dir}/bifrost/test_data/samples/S1_R1.fastq.gz"
     r2 = f"{bifrost_install_dir}/bifrost/test_data/samples/S1_R2.fastq.gz"