From afd67411663efa9c9b9ef21a2ca45883bb1f9a86 Mon Sep 17 00:00:00 2001
From: David Twesigomwe <38982270+twesigomwedavid@users.noreply.github.com>
Date: Wed, 8 Dec 2021 08:55:13 +0200
Subject: [PATCH] Update regions denotation

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index abcf98f..2b4ad67 100644
--- a/main.nf
+++ b/main.nf
@@ -103,7 +103,7 @@ process deepcall {
                 --reads  $bam  \
                 --output_vcf $vcf \
                 --num_shards 16 \
-                --regions chr$chrom
+                --regions ${params.chrom_prefix}$chrom
 
       """
 }
@@ -125,7 +125,7 @@ process phaseVCFs {
       /opt/exp_soft/python37/bin/whatshap phase \
         --output $phased_vcf \
         --reference  $ref_seq \
-        --chromosome $chrom \
+        --chromosome ${params.chrom_prefix}$chrom \
         $unphased \
         $bam
       tabix -p vcf $phased_vcf