Deal with genomes > 4 Gbp

Closes #81
sanger-tol · Nov 6, 2023 · 34e8eb2 · 34e8eb2
1 parent e09862e
commit 34e8eb2
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -53,7 +53,8 @@ process {
     }
 
     withName: '.*:.*:ALIGN_HIFI:MINIMAP2_ALIGN' {
-        ext.args = '-ax map-hifi --cs=short'
+        // For genomes larger than 4 Gbp, add the -I option with the genome size in Gbp
+        ext.args = { '-ax map-hifi --cs=short' + (meta.genome_size > 4294967296 ? (" -I" + Math.ceil(meta.genome_size/1073741824)+"G") : "") }
     }
 
     withName: '.*:.*:ALIGN_CLR:MINIMAP2_ALIGN' {