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.gitlab-ci.yml

@@ -30,7 +30,8 @@ getData:
     - push
     - tags
   except:
-    - merge_requests    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "master"
+    - merge_requests
+  script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bag/Replicate_Q-Y5F6.zip
   - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST
@@ -214,7 +215,8 @@ integration_se:
   stage: integration
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
@@ -237,7 +239,8 @@ integration_pe:
   stage: integration
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
@@ -261,7 +264,8 @@ override_inputBag:
   stage: integration
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
@@ -282,7 +286,8 @@ override_fastq:
   stage: integration
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
@@ -303,7 +308,8 @@ override_species:
   stage: integration
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
@@ -325,7 +331,8 @@ consistency:
   stage: consistency
   only: [merge_requests]
   except:
-    - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - grep -m 1 \"Assigned\":.[0-9] SE_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedSE.txt
   - grep -m 1 \"Assigned\":.[0-9] PE_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedPE.txt