diff --git a/nf-test.config b/nf-test.config index 69f28960..a1359d77 100644 --- 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 index 3d45039a..4dd1ad12 100644 --- 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 index 45c68854..77126cd5 100644 --- 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 = "$NCBI_KEY" + ncbi_email = "\$NCBI_EMAIL" + ncbi_key = "\$NCBI_KEY" } } diff --git a/tests/pipeline/test_mouse.nf.test b/tests/pipeline/test_mouse.nf.test index 69c9399e..071201ac 100644 --- a/tests/pipeline/test_mouse.nf.test +++ b/tests/pipeline/test_mouse.nf.test @@ -10,8 +10,8 @@ nextflow_pipeline { when { params { outdir = "$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 index 30fa5926..d14f3c16 100644 --- 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 = "$NCBI_KEY" + ncbi_email = "\$NCBI_EMAIL" + ncbi_key = "\$NCBI_KEY" } } diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test index c8f1c508..c6de1357 100644 --- a/tests/pipeline/test_taxa_specific_assembly.nf.test +++ b/tests/pipeline/test_taxa_specific_assembly.nf.test @@ -10,8 +10,8 @@ nextflow_pipeline { when { params { outdir = "$outputDir" - ncbi_email = "$NCBI_EMAIL" - ncbi_key = "$NCBI_KEY" + ncbi_email = "\\\$NCBI_EMAIL" + ncbi_key = "\\\$NCBI_KEY" } }