From b6580c830d31021754da8af79c53989ec0cbeef6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 May 2023 17:54:03 +0100
Subject: [PATCH] Fix workflow fails if job is not submitted (#10)

Changes:
 - 'export' was succeeding, so the workflow passed. Now separates to two
   steps which should fail properly.
 - Add failing test
---
 .github/workflows/ci.yml | 18 ++++++++++++++++++
 entrypoint.sh            |  4 ++--
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b450dff..41a3b5c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,6 +45,24 @@ jobs:
             | 😎 Workflow URL | ${{ steps.runs.outputs.workflowUrl }} |
           comment_tag: towerrun
         if: github.event_name == 'pull_request'
+      
+      - uses: ./
+        id: runfails
+        continue-on-error: true
+        with:
+          pipeline: no_pipeline_exists
+          revision: master
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          run_name: ${{ github.job }}_${{ github.sha }}
+          workdir: ${{ secrets.AWS_S3_BUCKET }}/work/${{ github.sha }}
+
+      - name: Check Failure
+        if: steps.runfails.outcome == 'success'
+        run: |
+          echo "Failed to catch invalid pipeline submission: ${{ steps.runfails.outcome }}"
+          exit 1
 
       - uses: actions/upload-artifact@v3
         with:
diff --git a/entrypoint.sh b/entrypoint.sh
index f7a83d4..ad6643c 100644
--- a/entrypoint.sh
+++ b/entrypoint.sh
@@ -33,7 +33,7 @@ if [ "$WAIT" = false ]; then unset WAIT; fi
 
 # Launch the pipeline
 # We use capture the JSON as variable $OUT. We encode it as base64 to get around Github secrets filters but we still mask it anyway to make sure the details don't leak.
-export OUT=$(tw -o json -v \
+OUT=$(tw -o json -v \
     launch \
     $PIPELINE \
     --params-file=params.json \
@@ -45,7 +45,7 @@ export OUT=$(tw -o json -v \
     ${PRE_RUN_SCRIPT:+"--pre-run=pre_run.sh"} \
     ${NEXTFLOW_CONFIG:+"--config=nextflow.config"} \
     ${WAIT:+"--wait=$WAIT"} \
-    2>> $LOG_FN | tee -a $LOG_FN | base64 -w 0)
+    2>> $LOG_FN | base64 -w 0)
 
 # Base64 decode and extract specific value for output
 export workflowId=$(echo $OUT | base64 -d | jq -r '.workflowId')