Bugfix: added missing refrence parameter

TRON-Bioinformatics · Feb 6, 2024 · 6daa929 · 6daa929
1 parent 00ff6ab
commit 6daa929
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -113,7 +113,7 @@ workflow {
         }
         if (params.algorithm == "aln"  && !params.inception) {
             BWA_ALN(trimmed_fastqs,params.reference)
-            BWA_SAMSE(BWA_ALN.out.alignment_output)
+            BWA_SAMSE(BWA_ALN.out.alignment_output,params.reference)
             output_bams = BWA_SAMSE.out.bams
         }
         else if (params.algorithm == "mem") {