make test profile use reads, test_nofastq use _nofastq csv

nf-core · Oct 29, 2024 · 01d7ced · 01d7ced
1 parent 5e88fd9
commit 01d7ced
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -24,4 +24,7 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'genomeqc/samplesheet/input_bacteria.csv'
 
+    // Run meryl+merqury
+    merqury_skip = false
+
 }
diff --git a/conf/test_merqury.config → conf/test_nofastq.config b/conf/test_merqury.config → conf/test_nofastq.config
@@ -22,9 +22,9 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'genomeqc/samplesheet/input_bacteria.csv'
+    input  = params.pipelines_testdata_base_path + 'genomeqc/samplesheet/input_bacteria_nofastq.csv'
 
-    // Run meryl+merqury
+    // Don't try to skip merqury, but since you don't have reads, it shouldn't get run anyway
     merqury_skip = false
 
 }
diff --git a/nextflow.config b/nextflow.config
@@ -24,7 +24,7 @@ params {
     groups                     = 'all'
 
     // merqury/meryl options
-    merqury_skip               = true
+    merqury_skip               = false
     kvalue                     = 21
 
     // BUSCO options
@@ -191,7 +191,7 @@ profiles {
         executor.memory         = 8.GB
     }
     test         { includeConfig 'conf/test.config'         }
-    test_merqury { includeConfig 'conf/test_merqury.config' }
+    test_nofastq { includeConfig 'conf/test_nofastq.config' }
     test_full    { includeConfig 'conf/test_full.config'    }
 }