Try getting github secrets in nf-test

nf-core · Apr 24, 2024 · 383e49a · 383e49a
1 parent 0d30528
commit 383e49a
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Showing 6 changed files with 13 additions and 12 deletions.
diff --git a/nf-test.config b/nf-test.config
@@ -1,5 +1,3 @@
-config {
-
 config {
     // location for all nf-tests
     testsDir "tests"
@@ -15,6 +13,6 @@ config {
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
-}
 
 }
+
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -1 +1,4 @@
-// Impose same minimum Nextflow version as the pipeline for testing
+//env {
+//    NCBI_EMAIL = '\$"\u007B""\u007B" NCBI_EMAIL "\u007D""\u007D"'
+//   NCBI_KEY   = '\$"\u007B""\u007B" NCBI_KEY "\u007D""\u007D"'
+//    }
diff --git a/tests/pipeline/test_all.nf.test b/tests/pipeline/test_all.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_mouse.nf.test b/tests/pipeline/test_mouse.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_taxa_only.nf.test b/tests/pipeline/test_taxa_only.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
             }
         }
 

diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test
@@ -10,8 +10,8 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                ncbi_email = "$NCBI_EMAIL"
-                ncbi_key = "$NCBI_KEY"
+                ncbi_email = "\\\$NCBI_EMAIL"
+                ncbi_key = "\\\$NCBI_KEY"
             }
         }