try creating .env file in pipeline

ktmeaton · Sep 30, 2020 · 6a95ee1 · 6a95ee1
1 parent 700620e
commit 6a95ee1
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/.github/workflows/pipeline.yaml b/.github/workflows/pipeline.yaml
@@ -67,13 +67,22 @@ jobs:
         shell: bash -l {0}
         run:
           mamba env create -f workflow/envs/default.yaml;
+      # Set up .env file with secrets
+      - name: create .env file
+        run:
+          echo "export SLACK_TOKEN=${{ secrets.SLACK_SNAKEMAKE }}" > .env
       #------------------------------------------------------------------------#
       # Test Data Download
       - name: test download
         shell: bash -l {0}
         run:
           conda activate default;
-          snakemake --profile profiles/gh-actions --use-conda --conda-frontend mamba test_download_ref test_download_fna test_download_sra test_download_gff test_download_gbff;
+          snakemake \
+            --profile profiles/gh-actions \
+            --use-conda \
+            --conda-frontend mamba \
+            --log-handler-script workflow/scripts/slack_log.py \
+            test_download_ref test_download_fna test_download_sra test_download_gff test_download_gbff;
           conda deactivate
       # Test Eager tsv
       - name: test eager tsv