refactor: Make fasttree the default (#44)

* refactor: Make fasttree the default * test: Use fasttree in test
beiko-lab · Feb 21, 2023 · b3a3ffa · b3a3ffa
1 parent 300f524
commit b3a3ffa
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -23,7 +23,7 @@ params {
     input_sample_table = "https://raw.githubusercontent.com/beiko-lab/arete/master/test/test_dataset.csv"
     use_bakta = false
     db_cache = false
-    use_full_alignment = true
+    use_full_alignment = false
     use_fasttree = true
     skip_kraken = true
 }

diff --git a/nextflow.config b/nextflow.config
@@ -17,7 +17,7 @@ params {
 
     // Phylogenomics parameters
     use_full_alignment         = false
-    use_fasttree               = false
+    use_fasttree               = true
 
     // Annotation parameters
     use_bakta                  = null

diff --git a/tests/subworkflows/local/phylo.nf.test b/tests/subworkflows/local/phylo.nf.test
@@ -19,10 +19,10 @@ nextflow_workflow {
                     [[id:'SRR14022764'], '$baseDir/test/SRR14022764_T1.gff'],
                     [[id:'SRR14022754'], '$baseDir/test/SRR14022754_T1.gff']
                 ])
-                // Use full alignment
-                input[1] = true
-                // Don't use fasttree
-                input[2] = false
+                // Don't use full alignment
+                input[1] = false
+                // Use fasttree
+                input[2] = true
                 """
             }
         }