Try new method.

Author: sdhutchins

.test/run_test.sh

@@ -23,8 +23,13 @@ cd ../workflows/FRASER_snakemake
 echo "🧹 Cleaning up previous test outputs..."
 rm -rf fraser_test_output fraser_test_input
 rm -rf .snakemake
+rm -rf logs
 
-./run_snakemake.sh --config_file "../../.test/config/test_config.yaml" --profile "config/slurm_scg"
+# Force Snakemake to run by using --forceall
+echo "🔧 Using --forceall to force pipeline execution..."
+
+# Run Snakemake directly with --forceall to force execution
+micromamba run -n snakemake7 snakemake --configfile "../../.test/config/test_config.yaml" --profile "config/slurm_scg" --use-conda --snakefile workflow/Snakefile --forceall
 
 echo "✅ Test completed successfully!"
 echo "Logs are available in: $(pwd)/logs/"