diff --git a/conf/test_align.config b/conf/test_align.config
index 8da6b65..f76a21b 100644
--- a/conf/test_align.config
+++ b/conf/test_align.config
@@ -21,6 +21,7 @@ params {
 
     // Input data
     input  = "${projectDir}/assets/samplesheet_test_align.csv"
+    align  = true
 
     // Fasta references
     fasta = "https://tolit.cog.sanger.ac.uk/test-data/Cantharis_rufa/assembly/GCA_947369205.1_OX376310.1_CANBKR010000003.1.fasta.gz"
diff --git a/conf/test_full_align.config b/conf/test_full_align.config
index 79b9fd7..a29005a 100644
--- a/conf/test_full_align.config
+++ b/conf/test_full_align.config
@@ -18,6 +18,7 @@ params {
 
     // Input data for full size test
     input = "${projectDir}/assets/samplesheet_test_full_align.csv"
+    align = true
 
     // Fasta references
     fasta = "/lustre/scratch124/tol/projects/darwin/data/insects/Polyommatus_icarus/assembly/release/ilPolIcar1.1/insdc/GCA_937595015.1.fasta.gz"