updated test configs

phac-nml · Apr 2, 2024 · 2b8de97 · 2b8de97
1 parent bebcbb3
commit 2b8de97
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Showing 2 changed files with 18 additions and 2 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -20,5 +20,13 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/samplesheet.csv'
+    input  = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/samplesheets/samplesheet1.csv'
 }
+
+
+/* This is required to run in WSL/Ubuntu using singularity
+Without this, profile_dists was not successfully completing
+due to issues with multiprocessing in the container. A similar
+error is found at https://github.com/marcelm/cutadapt/issues/583
+*/
+singularity.runOptions = "--contain"
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,5 +15,13 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/samplesheet.csv'
+    input = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/samplesheets/samplesheet1.csv'
 }
+
+/* This is required to run in WSL/Ubuntu using singularity
+Without this, profile_dists was not successfully completing
+due to issues with multiprocessing in the container. A similar
+error is found at https://github.com/marcelm/cutadapt/issues/583
+*/
+singularity.runOptions = "--contain"
+