add condition to run miniasm on long/hybrid mode only

nf-core · Sep 18, 2024 · 92bcfde · 92bcfde
1 parent 663a770
commit 92bcfde
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
@@ -240,7 +240,7 @@ workflow BACASS {
     //
     // MODULE: Miniasm, genome assembly, long reads
     //
-    if ( params.assembler == 'miniasm' ) {
+    if ( params.assembly_type != 'short' && params.assembler == 'miniasm' ) {
         MINIMAP2_ALIGN (
             ch_for_assembly.map{ meta,sr,lr -> tuple(meta,lr) },
             [[:],[]],
@@ -280,6 +280,8 @@ workflow BACASS {
         )
         ch_assembly = ch_assembly.mix( RACON.out.improved_assembly.dump(tag: 'miniasm') )
         ch_versions = ch_versions.mix( RACON.out.versions )
+    } else if (params.assembly_type == 'short' && params.assembler == 'miniasm') {
+        exit("Selected assembler ${params.assembler} cannot run on short reads")
     }
 
     //