From 7f9124e4981262575b053b7af795096f93ad7cf4 Mon Sep 17 00:00:00 2001
From: Magnus Wahlberg <endast@gmail.com>
Date: Fri, 17 May 2024 11:34:40 +0200
Subject: [PATCH] update

---
 .github/workflows/run-pipeline.yml |  2 +-
 .github/workflows/smoke-tests.yml  | 17 +++++++++--------
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml
index d9f6dd04..b443c719 100644
--- a/.github/workflows/run-pipeline.yml
+++ b/.github/workflows/run-pipeline.yml
@@ -28,7 +28,7 @@ jobs:
             cache-environment: true
             cache-downloads: true
         - name: Run pre pipeline cmd
-          if: prerun_cmd
+          if: inputs.prerun_cmd
           run: ${{inputs.prerun_cmd}}
           shell: bash -el {0}
         - name: ${{inputs.name}}
diff --git a/.github/workflows/smoke-tests.yml b/.github/workflows/smoke-tests.yml
index 51b6713e..ab54dff5 100644
--- a/.github/workflows/smoke-tests.yml
+++ b/.github/workflows/smoke-tests.yml
@@ -2,16 +2,17 @@ name: DeepRVAT Pipeline tests
 run-name: DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬
 on: [ push ]
 
+
 jobs:
   Smoke-RunTraining:
-    steps:
-      uses: ./.github/workflows/run-pipeline.yml
-      with:
-        environment_file: ./deeprvat_env_no_gpu.yml
-        name: Smoke-RunTraining
-        pipeline_cmd: |
-              python -m snakemake -n -j 2 --directory ./example \
-              --snakefile ./pipelines/run_training.snakefile --show-failed-logs
+    uses: ./.github/workflows/run-pipeline.yml
+    with:
+      environment_file: ./deeprvat_env_no_gpu.yml
+      name: Smoke-RunTraining
+      pipeline_cmd: |
+            python -m snakemake -n -j 2 --directory ./example \
+            --snakefile ./pipelines/run_training.snakefile --show-failed-logs
+    
 
 #  Pipeline-Tests-RunTraining:
 #    needs: Smoke-RunTraining