Updates for sanger testing

sanger-tol · Sep 20, 2023 · d7a448f · d7a448f
1 parent cad8ea6
commit d7a448f
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Showing 6 changed files with 2 additions and 114 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -43,9 +43,9 @@ jobs:
       - name: Run RAPID pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile github_test,docker --outdir ./results-rapid
+          nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile test,docker --outdir ./results-rapid
 
       - name: Run FULL pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile github_test,docker --outdir ./results-full
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results-full
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
diff --git a/assets/github_testing/TreeValTinyTest-Local.yaml b/assets/github_testing/TreeValTinyTest-Local.yaml
diff --git a/conf/github_test.config b/conf/github_test.config
diff --git a/conf/local_github_test.config b/conf/local_github_test.config
diff --git a/nextflow.config b/nextflow.config
@@ -154,8 +154,6 @@ profiles {
 
     test                    {   includeConfig 'conf/test.config'         }
     test_full               {   includeConfig 'conf/farm_test.config'         }
-    github_test             {   includeConfig 'conf/github_test.config'       }
-    local_github_test       {   includeConfig 'conf/local_github_test.config' }
 }