Activate env from script

BCCDC-PHL · Feb 8, 2024 · d0e3dbe · d0e3dbe
1 parent e56e45a
commit d0e3dbe
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/.github/scripts/simulate_reads.sh b/.github/scripts/simulate_reads.sh
@@ -1,6 +1,12 @@
 #!/bin/bash
 
 
+source ${HOME}/.bashrc
+
+eval "$(conda shell.bash hook)"
+
+conda activate art
+
 art_illumina \
     --paired \
     --in .github/data/assemblies/NC_000962.3.fa \

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -6,6 +6,9 @@ on:
 name: Pull Request
 jobs:
   test:
+    strategy:
+      matrix:
+        nextflow_version: [21.04, 23.10]
     name: Run tests
     runs-on: ubuntu-latest
     steps:
@@ -21,7 +24,7 @@ jobs:
     - name: Download Assemblies
       run: bash .github/scripts/download_assemblies.sh
     - name: Simulate Reads
-      run: conda init && source ~/.bashrc && conda activate art && bash ./github/scripts/simulate_reads.sh
+      run: bash ./github/scripts/simulate_reads.sh
     - name: Upload Artifacts
       uses: actions/upload-artifact@v4
       if: always()