try it in script again, not sure why this fails

schneebergerlab · Dec 12, 2024 · 03af7db · 03af7db
1 parent ce43346
commit 03af7db
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diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
@@ -15,5 +15,4 @@
 ## run using source to preserve alias
 #source ./example/example_workflow.sh
 
-$(tail -n +2 ./example/example_workflow.sh |\
-	sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/' )
+$(tail -n +2 ./example/example_workflow.sh | sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/'  -e 's/^minimap2/.\/minimap2/' )
diff --git a/.github/workflows/test_example.yml b/.github/workflows/test_example.yml
@@ -27,6 +27,5 @@ jobs:
         mv minimap2-2.28_x64-linux\/minimap2 ./
         ./minimap2 -h # test it worked & is callable
     - name: Test example_run.sh
-      run: |
-        $(tail -n +2 ./example/example_workflow.sh | sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/'  -e 's/^minimap2/.\/minimap2/' )
+      run: ./run_test_example.sh
       shell: bash