Run snakemake using Github action

Snitkin-Lab-Umich · Jan 21, 2025 · abb8756 · abb8756
1 parent 430c17d
commit abb8756
Showing 1 changed file with 12 additions and 11 deletions.
diff --git a/.github/workflows/test_pipeline.yml b/.github/workflows/test_pipeline.yml
@@ -137,16 +137,17 @@ jobs:
       #   uses: mxschmitt/action-tmate@v3
 
       - name: Snakemake workflow
-        run: |
-          source $CONDA/bin/activate
-          conda activate qcd_env_test
-          snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 
+        # run: |
+        #   source $CONDA/bin/activate
+        #   conda activate qcd_env_test
+        #   snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 
         # uses: snakemake/[email protected]
-        # with:
-        #   directory: '.'
-        #   snakefile: 'QCD.smk'
-        #   # stagein: ./mconfig --without-suid && \
-        #   #         make -C ./builddir && \
-        #   #         make -C ./builddir install
-        #   args: '--cores 4 --use-conda --use-docker --use-envmodules --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --singularity-args "--fakeroot"'
+        with:
+          directory: '.'
+          snakefile: 'QCD.smk'
+          # stagein: ./mconfig --without-suid && \
+          #         make -C ./builddir && \
+          #         make -C ./builddir install
+          task: 'containerize'
+          args: '--cores 4 --use-conda --use-singularity --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000' 
         #run: echo "🍏 This job's status is ${{ job.status }}."