diff --git a/software/ivar/consensus/main.nf b/software/ivar/consensus/main.nf index 54ea8f8a..bf326205 100644 --- a/software/ivar/consensus/main.nf +++ b/software/ivar/consensus/main.nf @@ -36,7 +36,7 @@ process IVAR_CONSENSUS { -aa -A -d 0 -Q 0 \\ $options.args2 \\ $bam | \\ - tee ${prefix}_mpileup.txt | \\ + $save_mpileup \\ ivar consensus \\ $options.args \\ -p $prefix