use reference for mpileup for ivar #28

TRON-Bioinformatics · Nov 19, 2022 · 7d7c6e3 · 7d7c6e3
1 parent 8a14ae2
commit 7d7c6e3
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/modules/04_variant_calling.nf b/modules/04_variant_calling.nf
@@ -141,6 +141,7 @@ process VARIANT_CALLING_IVAR {
     --redo-BAQ \
     --min-BQ ${params.min_base_quality} \
     --min-MQ ${params.min_mapping_quality} \
+    --fasta-ref ${reference} \
     ${bam} | \
     ivar variants ${params.args_ivar} \
     -p ${name}.ivar \